March 2014 - Allocations-admins - mailman3.cels.anl.gov

[LCRC Accounts] Project Request: lipidmovement
by accounts＠lcrc.anl.gov 20 Mar '14

20 Mar '14

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: Ursula Perez Salas Applicant's institution: ANL Applicant's division: MSD Project Name: lipidmovement Project title: Curvature Effect on the Movement of Lipids Within and Between Membranes Associated funding: LDRD Other Systems: UIC extreme cluster Science: This project uses Molecular Dynamics simulations to investigate the diffusion of lipids, specifically DMPC and cholesterol, in curved lipid membranes. We will calculate the free energy profile of extraction as well as flip-flop in a curved lipid membrane, i.e. a vesicle. The results will be compared to those obtained from MD simulations on planar membranes, which agree with experimental data of planar membranes but disagree substantially from data on highly curved lipid vesicles. The curvature is expected to affect the transfer rate of lipids into the membrane as well as its movement across lipid leaflets. The results will provide an atomic-level explanation for different kinetic rates obtained in small angle neutron scattering experiments. The movement of lipids within membranes (flip-flop) together with the exchange between membranes under physiological conditions allows the creation of asymmetric distributions of lipids across cellular membranes. Further, the location of lipids and their rate of exchange have important biological consequences, especially for lipids involved in cellular signaling. Therefore decoding the underlying mechanisms that control lipid transfer between and within lipid membranes is critical for understanding lipid homeostasis in the cell as well as the metabolic pathways that sustain it. The proposed research seeks to identify key physical membrane properties, specifically curvature, which govern both exchange and flip-flop of lipids in membranes. Project description: We will use a coarse-grained description of the system using the MARTINI force field to create lipid vesicles of various diameters solvated in water. Cholesterol will be added to the system at extremely low and high concentrations, which will then partition into the lipid vesicle. A vesicle of 30 nm diameter results in a system of approximately 1M particles. The free energy profile across bilayer for a lipid is then calculated using the umbrella sampling technique. In this technique the phase space is divided into many small regions, which are sampled independently and then combined using the Weighted Histogram Analysis method to provide a single energy profile. In addition to the free energy profiles, long simulations will be run in order to directly observe the lipid movement. We will use the molecular dynamics program NAMD, which is developed at University of Illinois at Urbana-Champaign and is freely available for download (http://www.ks.uiuc.edu/Research/namd/) NAMD is highly parallel and scales efficiently with the number of particles in the system. Preliminary simulations of the system at the UIC cluster has shown a benchmark of 130ms/timestep on 64 cores. Using a time step of 20fs, we estimate that the proposed calculations require approximately 4 microseconds of simulation requiring a total of 460,000 core-hours. Project URL: Requested allocation: 460000 Q1: 115000 Q2: 115000 Q3: 115000 Q4: 115000 Justification: The requester has used undetermined amount 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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[LCRC Accounts] Project Request: LowF_VRC-TST
by accounts＠lcrc.anl.gov 19 Mar '14

19 Mar '14

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: Marco Verdicchio Applicant's institution: ANL Applicant's division: CSE Project Name: LowF_VRC-TST Project title: Low frequencies modes coupling in Variable Reaction Coordinate TST Associated funding: DOE-BES Other Systems: pople.tcg.anl.gov, linus.tcg.anl.gov Science: Radical-radical association reactions and unimolecular dissociations to free radicals are known to be of great importance in the chemistry of hydrocarbons combustion and planetary atmospheres. This kind of reactions, however, often show very low or absent local potential energy barrier, which makes traditional Transition State Theory (TST) calculations unfeasible. The variable reaction coordinate (VRC) TST approach has been proven to be of considerable utility in estimating the kinetic of barrierless reactions. The transition state dividing surface, defined by a fixed distance between a set of pivot points on each fragment, provide a valuable approximate division of the phase space into reactants and products. The position of each pivot in the molecular frame of the corresponding fragment determines the shape of the dividing surface. The optimization of both pivot point locations and distances between them provides a great flexibility in the definition of the dividing surface and allow the investigation of multiple binding sites system (i.e. addition reactions of resonantly stabilized, multiple side attack radical additions, etc.). A common problem for reactions involving radicals is the presence of a low frequency umbrella mode that is poorly treated in the harmonic oscillator approximation. Moreover this mode is often coupled to torsional modes and it is not clear how this coupling affect the partition functions. Our goal, in this project, is to develop and apply a new computational method to efficiently handle the large anharmonicities arising in molecule with strong coupled low frequencies modes. We propose to explore these issues for a number of prototypical radical-radical association reactions relevant in combustion and atmospheric chemistry. Project description: - Computational methods: We intend to use VRC-TST theory to study the effect of coupled low frequencies motions on EJ-resolved, microcanonical and canonical kinetic constants for several radical-radical association reactions. In this first stage of the project*, the following systems will be taken into consideration: - C2H5 + H - CH3 + CH3 - CH3 + CH2OH - C2H5 + O2 (*Extension and optimization of the method for larger chemical systems is also a crucial point.) The central focus of VRC-TST is the evaluation of the reactive flux through an arbitrary dividing surface for several temperatures. In particular a multifaceted dividing surface approach, which allow for the incorporation of multiple dividing surfaces for each binding site, will be adopted. This scheme allows high flexibility on the dividing surface shape and the possibility to take into account additional reaction pathways (i.e. H atom abstraction). Unfortunately the computational cost of each kinetic calculation increases with the number of considered dividing surfaces. A variational minimization of the reactive flux is then performed with respect to both the location of the pivot points and the distances between them. In order to evaluate the effect of the coupling of the two low frequencies modes on the kinetic constant we will compute the reactive flux for different values of torsional angle (Phi) and umbrella bending (Chi). This step requires the generation of a large set of independent VRC-TST kinetic calculations one for each value of the couple [Phi, Chi]. The final kinetic constant is then obtained by integrated (with proper weight functions for each point) over Phi and Chi. To provides a suitable description of the torsional and umbrella motion potentials, and to include Complete Basis Set limit corrections to the potential energy, preliminary quantum chemistry ab initio calculations are also necessary (about 10000 cpu/hours). - Technical details: Kinetic calculations will be performed using the VRC-TST method as implemented in the computer code VaReCoF (Y. Georgievskii, S.J. Klippenstein, VaReCoF, Sandia National Laboratories and Argonne National Laboratory, 2006). The code makes use of the MOLPRO or GAUSSIAN quantum chemistry software for on-the-fly evaluation of the potential energy. A Python interface to the code has been implemented for the management of the input files (reference energy evaluation, pivot points positions, etc.), for the generation of the input different structures ([Phi,Chi] grid of points) and for results post processing. The code does not require large amount of memory (less than 1GB) and works very efficiently on parallel architectures. The code makes use of MPI and shows a speed-up efficiency of about 60% for up to 96 CPU’s (test performed on a 8 cpu/cores AMD Operton 2354 machine). Improvement is expected with better CPUs and fastest internode connections. - Expected number of project members: 3 Project URL: Requested allocation: 85000 Q1: 0 Q2: 0 Q3: 35000 Q4: 50000 Justification: The requester has used undetermined amount 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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[LCRC Accounts] Project Request: MD_for_riboA
by accounts＠lcrc.anl.gov 19 Mar '14

19 Mar '14

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: Bachir Aoun Applicant's institution: ANL Applicant's division: XSD Project Name: MD_for_riboA Project title: Molecular Dynamics Simulation of the unbounded Adenine Riboswitch RNA Associated funding: BES/DOE Other Systems: No Science: The main objective of this proposal is to use computer simulations to characterize molecular processes in riboswitch ribonucleic acid (RNA), make direct connections to solution x-ray scattering results, and better understand the structural and dynamic properties key to its biological function. For a long time, all RNAs but tRNA, mRNA, and rRNA that involve protein synthesis had been considered junk material in biological organisms. However, in the past two decades, these non-coding RNAs have been discovered to play pivotal biological roles, such as catalysis and gene regulation, many of which had been thought only capable of being performed by its counterpart, protein. Despite their biological importance, knowledge of three dimensional structural details of RNAs is very limited due to the characterization difficulties in RNA structure determination . This project uses the molecular dynamics (MD) simulation method to model solution state structures of the unbounded aptamer domain of adenine riboswitch RNA molecule. Riboswitch RNAs are gene-regulatory, non-coding RNA elements found in bacteria, fungi and plants and are likely candidates for drug-targets. Adenine riboswitch RNA was found in the add gene of Bacillus subtilis. The aptamer domain of adenine riboswitch RNA has 71 nucleotides (riobA71), and the structure and dynamics of the unbounded riboA71 is closely connected to the RNA’s function. However, in general, the inherit flexibility of the unbounded RNA states makes it difficult to extract atomistically detailed information from most standard characterization tools. Solution x-ray scattering is a powerful structural characterization tool capable of measuring spatial information from all atoms within large molecules; however, its resolution is relatively low due to the isotropic nature of solution phase samples. MD simulations, on the other hand, can provide detailed molecular-level information and probe dynamical processes. The results from the herein proposed MD simulations will be coupled with x-ray scattering measurements to generate a unifying picture of this complex system and help elucidate the structure and dynamics of riboA71. We have already measured riboA71 under various conditions using solution x-ray scattering and obtained low-resolution envelopes for the RNA. We expect this combined simulation and experimental characterization study will generate a strong feedback loop between theory and experiment to obtain an atomic level delineation on the riboswitch RNA’s structure and dynamics (e.g. identification of base pairs key to open/close mechanism, structure and accessibility of binding sites, structural evolution in different salt environments) and ultimately provide structural insights into RNA structure-function relationships. Project description: In this project, adenine riboswitch RNA will be investigated using the molecular dynamics simulation method. Adenine riboswitch RNA consists of an aptamer domain and an expression platform domain which partially overlap each other in sequence. The aptamer domain binds to an adenine ligand and leaves the translation promoter, the Shine-Dalgarno sequence, in the expression platform domain accessible to the translation apparatus starting the translation process. The crystal structural adenine-bounded aptamer domain has been solved in 2005 and many mutagenesis studies have been performed on the bounded structures since then. The extensive studies on the bounded aptamer domain make it a model system for an RNA structural study. However, unbound states, which are important for understanding the RNA function, have been less studied due to technical difficulties discussed above. Recently, we have employed solution x-ray scattering technique to study the apta mer domain of riboA71 under various conditions, including with and without adenine, MgCl2, and urea, and successfully obtained the low-resolution molecular envelope of riboA from the scattering data . In this project, we plan to perform the molecular dynamics simulation on riboA71 under the same experimental conditions. The purpose of this project is three folds: (1) providing a atomistic structural picture of the unbounded riboA71 and insights into the RNA function; (2) trying to find the governing principles for the structure and dynamics key to RNA folding; (3) providing a solid foundation for near-future projects focused on the adenine ligand capture process for the aptamer domain and the full length RNA. Currently, we have done some short time simulations on a small cluster and observed encouraging agreement with x-ray scattering measurements. For example, the RNA structure was successfully reproduced for the case of no adenine and Mg2+ within a 10 nanosecond (ns) simulation, but it is imperative to run a longer (80-100 ns) simulation to check convergence of equilibrium properties, such as structure stability, and sample long-time dynamical modes of the system. We are currently in the position to immediately begin running simulations at the start of the award period for these important simulations. The MD simulations in this project will calculated using the NAMD code, which has been ported to several high-performance computing architectures and is efficiently parallelized for large-scale computations. In total, 10 systems of varying salt concentrations and ligands will be simulated to make a direct comparison to the experimental characterization results. Each simulation requires 100 ns to obtain statistically converged results. The parallel efficiency of the NAMD code using the riobA71 system currently being examined (47,582 particles) was determined to be 85.2% and 58.2% on 256 and 512 Intel Sandy Bridge cores, respectively. On 512 cores, with a productivity of 29.16 ns/day each 100 ns trajectory would require 42,140 core-hours. Thus, the total allocation request encompassing all ten planned simulations brings the total allocation request to 421,400 core-hours with a nearly linear burn-rate over the course of the award period. The herein planned simulations will be managed by Bachir Aoun (XSD) and Chris Knight (LCF), both of whom have extensive experience with running molecular simulations. Xiaobing Zuo (XSD) has performed the x-ray scattering measurements and will be involved in all discussions regarding the comparisons between simulated and experimental characterizations of these riboA71 systems. Project URL: Requested allocation: 421400 Q1: 105350 Q2: 105350 Q3: 105350 Q4: 105350 Justification: The requester has used undetermined amount 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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[LCRC Accounts] Project Allocation Request
by accounts＠lcrc.anl.gov 19 Mar '14

19 Mar '14

Hello, A change in allocation has been requested: Requester: dduke (Daniel Duke) Project: XRayFuelSpray Title: Fuel Injection and Sprays Studied Using X-Ray Diagnostics Description: Computational Fluid Dynamics using the OpenFOAM framework has been employed to simulate cavitating turbulent fluid flow in both simplified nozzles and diesel fuel injectors, with the purpose of supporting and informing x-ray radiography and phase-contrast measurements performed at the Advanced Photon Source. A number of state-of-the-art numerical solvers have been implemented in OpenFOAM; namely incompressible-liquid and fully compressible homogeneous relaxation cavitation models and more recently a noncondensible-gas fully compressible homogeneous relaxation cavitation model. These codes were developed by Schmidt et al at the University of Massachusetts-Amherst. In the last year, we have switched from using OpenFOAM’s built-in solvers for multiphase flow to a dedicated cavitation code (HRMFoam) developed by Professor David Schmidt. The homogeneous relaxation model (HRM) assumes that when vapor is present, the vapor and liquid are homogeneously mixed within the local cell, but are not at thermodynamic equilibrium. The equilibrium state is not computed using an equation of state but is instead determined from a lookup table formulated using NIST REFPROP data. The HRM model has successfully been employed to simulate the effect of varying gasoline-ethanol blended fuels in a cavitating polycarbonate nozzle, and the results were favorably compared to x-ray radiography measurements performed at the Advanced Photon Source. Further high-resolution large eddy simulations of the polycarbonate nozzles used at APS are need to be undertaken in the following year. Scalability of HRMFoam simulations is good up to approx. 72 processors (the capacity of our dedicated nodes). We need to run multiple simulations at various boundary conditions, thus the need for additional allocation beyond the use of the dedicated nodes. Several improved solvers are currently under development which over the next year will allow for the modeling of a non-condensible gas phase, to simulate the difference between a ‘submerged’ cavitating flow and a cavitating flow issuing into a gaseous environment, as is the case for fuel injection in engines. Compressible modeling is also being investigated through both HRM and also alternative compressible fluid solvers. Currently, HRM assumes the liquid phase to be incompressible. Although this has shown good results in comparison with experimental data, given the extremely high pressures involved in fuel injection (greater than 1500 bar) bulk compressibility of the fuel will not be insignificant. Further development is occurring within the OpenFOAM framework and we do not expect to need any additional software installed on Fusion to achieve these goals. Our allocation for the following year will need to be maintained at the current level to achieve the above goals. No increase in allocation is required. We expect that less than 1% of the allocation will be single-core jobs (of which most are file I/O and cleanup tasks at the start and end of parallel jobs). Current: undetermined amount Justification: 6*12 processor dedicated nodes have been purchased on FUSION to support these studies. Requested: 15000 A specific reason has been given: We have several simulations currently running on fusion and blues which need to be completed before the end of the current allocation period. We also need to run tests of a new build of OpenFOAM which will require some extra hours. As our allocation is almost exhausted for this period, we require extra core-hours for the current allocation period only, in order to complete these tasks. This needs to be approved and the final allocation amount decided upon. Thank You, The LCRC Accounts System

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[LCRC Accounts] Project Allocation Request
by accounts＠lcrc.anl.gov 18 Mar '14

18 Mar '14

Hello, A change in allocation has been requested: Requester: tslee (Tsung-Shung Lee) Project: anl-dcc Title: Dynamical coupled-channel analysis of hadrons at Argonne Description: In 2013, we have completed a 8-channel analysis with a publication accepted by Physical Review C, August 27, 2013. In 2014, we will extend this to include omega-N channel which is crucial in finalizing our determination of the nucleon spectrum at energies in the region of 1.8 - 2.5 GeV. This will allow us to analyze the new data from Jefferson Laboratory. The computations involve solving a large set of coupled-channel integral equations and searching for parameters to fit the world data of meson production of pion-nucleon and photon-nucleon reactions. The calculations account for eight meson-baryon channels and cover energies up to invariant mass W= 3 GeV. Large complex-matrix (1000 by 1000) need to be inverted many times in chi**2-fit to very extensive data (about 110,000 data points) . Standard fortran codes have been developed to perform parallel computations with the facilities at LCRC. The project will have 4 members. Current: undetermined amount Justification: Requested: 300000 A specific reason has been given: We will start production run in the coming April, which require extensive search of about 100 parameters to fit about 20,000 new data points from JLab to complete the ANL-Osaka project to reach DOE milestone HP7. This is the final stage of this 7-year DOE project on determining the excited nucleon states. This needs to be approved and the final allocation amount decided upon. Thank You, The LCRC Accounts System

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Re: [allocations-admins] [LCRC Accounts] Project Allocation Request
by Low, John J. 18 Mar '14

18 Mar '14

Alejandro, Are you sure you can use 450,000 core-hours by April 1st? It does not make sense to request more than you use can by April 1st because these hours will expire by April 1st. By the way, 450,000 is a large fraction of a million.... John -----Original Message----- From: allocations-admins-bounces(a)lists.lcrc.anl.gov [mailto:[email protected]] On Behalf Of accounts(a)lcrc.anl.gov Sent: Tuesday, March 18, 2014 1:21 PM To: allocations-admins(a)lcrc.anl.gov Subject: [allocations-admins] [LCRC Accounts] Project Allocation Request Hello, A change in allocation has been requested: Requester: albezanilla (Alejandro Lopez Bezanilla) Project: DopedDWNT Title: Transport Properties of doped carbon nanotubes Description: We will use the SIESTA code for the ab initio calculations, which provides an excellent performance as dealing with systems formed of about 1000 atoms. This code has been built by the LCRC support team and successfully tested in both Fusion and Blues. It is showing a high efficiency for the geometry relaxations and the calculations of the electronic structures. Current: undetermined amount Justification: Requested: 450000 A specific reason has been given: The current project is in negative balance. I need additional time to finish calculations to address the referees' concerns of my latest submitted paper 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)lists.lcrc.anl.gov https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins

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[LCRC Accounts] Project Allocation Request
by accounts＠lcrc.anl.gov 18 Mar '14

18 Mar '14

Hello, A change in allocation has been requested: Requester: albezanilla (Alejandro Lopez Bezanilla) Project: DopedDWNT Title: Transport Properties of doped carbon nanotubes Description: We will use the SIESTA code for the ab initio calculations, which provides an excellent performance as dealing with systems formed of about 1000 atoms. This code has been built by the LCRC support team and successfully tested in both Fusion and Blues. It is showing a high efficiency for the geometry relaxations and the calculations of the electronic structures. Current: undetermined amount Justification: Requested: 450000 A specific reason has been given: The current project is in negative balance. I need additional time to finish calculations to address the referees' concerns of my latest submitted paper This needs to be approved and the final allocation amount decided upon. Thank You, The LCRC Accounts System

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Re: [allocations-admins] [LCRC Accounts] Project Allocation Request
by Bair, Raymond A. 12 Mar '14

12 Mar '14

Looks OK to me, +100K for March. Ray On 3/12/14 5:46 PM, "accounts(a)lcrc.anl.gov" <accounts(a)lcrc.anl.gov> wrote: >Hello, > >A change in allocation has been requested: > > Requester: rajeev (Rajeev Surendran Assary) > Project: Cat_Biomass > Title: Computational Studies of Biomass Catalysis > Description: Catalytic C-O bond cleavage: >Efficient catalytic cleavage of C-O bonds of biomass molecules is crucial >to the conversion of biomass to transportation fuels and industrial >chemicals. Recently, we have explored a series of lanthanide trivalent >metal triflates as potential catalysts for the C-O bond cleavage in ionic >liquids using combined quantum chemical methods. This theoretical >finding is supported by the experimental studies. the metal triflate >catalysts were found to be active for a series of ether substrates When >used in tandem with hydrogenation catalysts (Pd/Alumina), etheric >substrates afford industrially useful alcohols. In this proposal we would >like to identify most efficient metal triflate catalysts for the >conversion of ethers to alcohols and subsequently to alkanes using >quantum chemical methods. This information regarding the catalysis can be >then feed into experimentalists for testing. For computations, the >density functional theory (DFT) will be used to compute various catalytic >descript > ors such as binding of ether substrates with the catalysts and the >activation energy required to cleave the C-O bonds of various substrates. >Calculations will also be performed to understand detailed reaction >mechanisms to identify undesired reactions and to improve the efficacy of >the catalyst by rational design. >Various metal triflate catalysts with central metal atoms (Z=22 to Z=92) >will be considered for this study. The oxidation states from +3 to +6 >will be considered. Due to bulkiness and bidentate nature of the triflate >ligands, upon coordination with highly positive metal ions (for example >Nb (V) or Mo(VI)), it is likely that the first coordination layer of the >central metal ion may be saturated by the triflate and the binding of >ether-substrate and subsequent catalysis may be unlikely. Here, we >propose to model such scenarios by mutating the ligands of M(OTf)n (n=4 >to 6) by less bulky mono anionic systems ( for e.g. F-, CN- etc.) and >compute the C-O bond breaking efficacy using DFT. >Catalytic C-C coupling: >Acidolysis or pyrolysis of biomass yields furans and Low Molecular Weight >Carbohydrates (LMWC, contains C1 to C4 compounds). In order to convert >these fragments to liquid transportation fuels, efficient C-C coupling is >essential. To address the C-C coupling between the fragments two types of >reactions are envisioned here, namely cyclo-addition reactions and aldol >type condensations. The cyclo-addition reactions can be thermal or >catalytic. First we will investigate detailed thermochemistry and >activation barriers of likely cyclo-addition reactions between furan and >LMWC (20-100 reactions) and rank these reactions based on thermodynamics >and kinetics. Selected reactions will be further studied using various >Lewis base catalysts to understand the catalysis and side reactions. >These Lewis acid catalysts can be either metal ions or metal ions >impregnated inside a porous cavity to provide a nano confinement for the >catalytic process. These confinement effects will be modeled to un > derstand their effects on catalytic reaction mechanisms. These >calculations taking account of the effects of porous frame work can be >computationally very demanding and we intend to perform combined Quantum >Mechanical/Molecular Mechanical (QM/MM) simulations and subsequent >periodic Carr-Parrinello Ab Initio Molecular Dynamics (CP-AIMD) >simulations for the modeling of catalytic process. > >Second category of C-C coupling reactions that we would like to address >is Aldol reaction combined with hydro cyclo addition reactions. The >reaction sequence here is aldol reaction, hydrogenation in tandem with >cyclo-addition reactions. >In principle, these cascades of reactions can convert furans (C4-C6) to >diesel fuels range chemicals (C14-C16). Two major challenges here are >liquid phase hydrogenation of the aldol products and selectivity of >hydrocycloaddition reactions. To address these challenges, first, we >intend to understand the energy landscapes (including reaction barriers) >of these reaction networks using accurate quantum chemical methods (G4 >methods, CCSD(T)). Using this valuable information, we intend to perform >dynamic simulations including the effects of explicit solvent molecules >and various base catalysts (Lewis base) for aldol reactions. Similar >calculations were indented to study liquid phase catalytic hydrogenation >as well. > >in terms of softwares, we intend to use Gaussian 09 and CPMD. The DFT >calculations of gaussian 09 is scalable up to 64 processors, while >high-level CCSD(T)-based calculations is only scalable up to 16 >processors and require long execustion time. The CPMD is a highly >parallelized code and is scalable up to 500 processors. >At the moment, the project has four members, Rajeev Assary, Larry >Curtiss, Cong Liu, and Stan Zigmunt. We are planning to hire one more >postdoc in the near future. > Current: undetermined amount >Justification: We have made excellent use of the previous allocation of >1.2 M core hours. The computations resulted in 11 high impact >publications during the 2012-13 allocation time. >Significant amount of calculatins were gaussian and CPMD based >calculations. gaussian calculations require longer running hours ( often >more than 48 hours). Additionally running 10s of gaussian jobs at a time >has been found really difficult during the previous allocation. >CPMD calculations were performed efficiently on 60 nodes (Fusion). We >expect to run similar calculations during this allocation. > > > Requested: 100000 > >A specific reason has been given: >The request (100K) is for till the end of March to run some essential >CCSD(T) calculations using NWChem > >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)lists.lcrc.anl.gov >https://lists.lcrc.anl.gov/mailman/listinfo/allocations-admins

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[LCRC Accounts] Project Allocation Request
by accounts＠lcrc.anl.gov 12 Mar '14

12 Mar '14

Hello, A change in allocation has been requested: Requester: rajeev (Rajeev Surendran Assary) Project: Cat_Biomass Title: Computational Studies of Biomass Catalysis Description: Catalytic C-O bond cleavage: Efficient catalytic cleavage of C-O bonds of biomass molecules is crucial to the conversion of biomass to transportation fuels and industrial chemicals. Recently, we have explored a series of lanthanide trivalent metal triflates as potential catalysts for the C-O bond cleavage in ionic liquids using combined quantum chemical methods. This theoretical finding is supported by the experimental studies. the metal triflate catalysts were found to be active for a series of ether substrates When used in tandem with hydrogenation catalysts (Pd/Alumina), etheric substrates afford industrially useful alcohols. In this proposal we would like to identify most efficient metal triflate catalysts for the conversion of ethers to alcohols and subsequently to alkanes using quantum chemical methods. This information regarding the catalysis can be then feed into experimentalists for testing. For computations, the density functional theory (DFT) will be used to compute various catalytic descript ors such as binding of ether substrates with the catalysts and the activation energy required to cleave the C-O bonds of various substrates. Calculations will also be performed to understand detailed reaction mechanisms to identify undesired reactions and to improve the efficacy of the catalyst by rational design. Various metal triflate catalysts with central metal atoms (Z=22 to Z=92) will be considered for this study. The oxidation states from +3 to +6 will be considered. Due to bulkiness and bidentate nature of the triflate ligands, upon coordination with highly positive metal ions (for example Nb (V) or Mo(VI)), it is likely that the first coordination layer of the central metal ion may be saturated by the triflate and the binding of ether-substrate and subsequent catalysis may be unlikely. Here, we propose to model such scenarios by mutating the ligands of M(OTf)n (n=4 to 6) by less bulky mono anionic systems ( for e.g. F-, CN- etc.) and compute the C-O bond breaking efficacy using DFT. Catalytic C-C coupling: Acidolysis or pyrolysis of biomass yields furans and Low Molecular Weight Carbohydrates (LMWC, contains C1 to C4 compounds). In order to convert these fragments to liquid transportation fuels, efficient C-C coupling is essential. To address the C-C coupling between the fragments two types of reactions are envisioned here, namely cyclo-addition reactions and aldol type condensations. The cyclo-addition reactions can be thermal or catalytic. First we will investigate detailed thermochemistry and activation barriers of likely cyclo-addition reactions between furan and LMWC (20-100 reactions) and rank these reactions based on thermodynamics and kinetics. Selected reactions will be further studied using various Lewis base catalysts to understand the catalysis and side reactions. These Lewis acid catalysts can be either metal ions or metal ions impregnated inside a porous cavity to provide a nano confinement for the catalytic process. These confinement effects will be modeled to un derstand their effects on catalytic reaction mechanisms. These calculations taking account of the effects of porous frame work can be computationally very demanding and we intend to perform combined Quantum Mechanical/Molecular Mechanical (QM/MM) simulations and subsequent periodic Carr-Parrinello Ab Initio Molecular Dynamics (CP-AIMD) simulations for the modeling of catalytic process. Second category of C-C coupling reactions that we would like to address is Aldol reaction combined with hydro cyclo addition reactions. The reaction sequence here is aldol reaction, hydrogenation in tandem with cyclo-addition reactions. In principle, these cascades of reactions can convert furans (C4-C6) to diesel fuels range chemicals (C14-C16). Two major challenges here are liquid phase hydrogenation of the aldol products and selectivity of hydrocycloaddition reactions. To address these challenges, first, we intend to understand the energy landscapes (including reaction barriers) of these reaction networks using accurate quantum chemical methods (G4 methods, CCSD(T)). Using this valuable information, we intend to perform dynamic simulations including the effects of explicit solvent molecules and various base catalysts (Lewis base) for aldol reactions. Similar calculations were indented to study liquid phase catalytic hydrogenation as well. in terms of softwares, we intend to use Gaussian 09 and CPMD. The DFT calculations of gaussian 09 is scalable up to 64 processors, while high-level CCSD(T)-based calculations is only scalable up to 16 processors and require long execustion time. The CPMD is a highly parallelized code and is scalable up to 500 processors. At the moment, the project has four members, Rajeev Assary, Larry Curtiss, Cong Liu, and Stan Zigmunt. We are planning to hire one more postdoc in the near future. Current: undetermined amount Justification: We have made excellent use of the previous allocation of 1.2 M core hours. The computations resulted in 11 high impact publications during the 2012-13 allocation time. Significant amount of calculatins were gaussian and CPMD based calculations. gaussian calculations require longer running hours ( often more than 48 hours). Additionally running 10s of gaussian jobs at a time has been found really difficult during the previous allocation. CPMD calculations were performed efficiently on 60 nodes (Fusion). We expect to run similar calculations during this allocation. Requested: 100000 A specific reason has been given: The request (100K) is for till the end of March to run some essential CCSD(T) calculations using NWChem This needs to be approved and the final allocation amount decided upon. Thank You, The LCRC Accounts System

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Re: [allocations-admins] [LCRC Accounts] Project Allocation Request
by John Valdes 07 Mar '14

07 Mar '14

This was me submitting a request for Gary; approving... John On Fri, Mar 07, 2014 at 04:08:26PM -0600, accounts(a)lcrc.anl.gov wrote: > Hello, > > A change in allocation has been requested: > > Requester: leaf (Gary Leaf) > Project: dynamics [...] > Requested: 80000

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