Could we allocate 100K to this project now and then review the full request and the next allocation meeting? ----- Original Message ----- From: "Sanket Avinash Deshmukh" <[email protected]> To: "John J. Low" <[email protected]> Sent: Thursday, July 28, 2011 10:17:02 AM Subject: Re: [lcrc-core] Fwd: [allocations-admins] [LCRC Accounts] Project Request: MD_solvent_mixtures Hi John, Yes, I will be glad to have any additional time you can give to me for this year. 100K or if possible more than 100K is also okay for this year. As per your suggestion I will apply for additional time next year. I am using LAMMPS molecular dynamics simulation package. So far I have used it on Carbon (CNM cluster) and on Fusion. It scales very well on Fusion for the polymer systems that I am studying. Thank you. Regards, Sanket On Jul 27, 2011, at 4:32 PM, John J. Low wrote:

Sanket,

It would be difficult to allocate 800K core-hours this fiscal year which ends this quarter. This is a large fraction of the core-hours available on Fusion until the end of the September (approximately 5M core-hours). It would be much easier to allocate 100K core-hours to this project for this quarter (until the end of September). You could request an additional 700K core-hours for next year. Would that be acceptable?

Please tell us what software you will be using in this project.

John J. Low Computational Scientist-STA Mathematics and Computer Science Building 240, 1.G.10 9700 South Cass Avenue Argonne National Laboratory Argonne, IL 60439. 630-252-0045

----- Forwarded Message ----- From: "John Valdes" <[email protected]> To: [email protected] Sent: Wednesday, July 27, 2011 2:41:24 PM Subject: [lcrc-core] Fwd: [allocations-admins] [LCRC Accounts] Project Request: MD_solvent_mixtures

----- Forwarded message from [email protected] -----

Date: Thu, 21 Jul 2011 13:32:47 -0500 (CDT) From: [email protected] To: [email protected] Subject: [allocations-admins] [LCRC Accounts] Project Request: MD_solvent_mixtures Reply-To: [email protected]

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: Sanket Deshmukh Applicant's institution: ANL Applicant's division: CNM Project Name: MD_solvent_mixtures Project title: Atomistic simulations to understand the effect of Water/Methanol Solvent Mixtures on the Lower Critical Solution Temperature of poly(N-isopropylacrylamide) Associated funding: Other Systems: Carbon (CNM) Science: PNIPAM is a thermo-sensitive polymer that has a lower critical solution temperature (LCST) around 305K in aqueous solution.1 As the LCST of PNIPAM is close to human body temperature, it is a serious contender for a controlled drug delivery system.2,3 Coil-to-globule transition occurs in PNIPAM when temperature is raised above the LCST. It is believed that this occurs due to the change in hydrophilic interaction to the hydrophobic interaction.1 Concentration and molecular weight of PNIPAM affects the LCST by less than 1K (304???306K). Lower molecular weight samples appear to have slightly higher LCST. On the other hand, the presence of salts ions in the solution lowers the LCST significantly.1,4 It is believed that, when PNIPAM is dissolved in solvent such as water, PNIPAM has to arrange itself in a specific orientation to form hydrogen bond with the already somewhat arranged water molecules.1 In the case of water molecules, which are near to hydrophobic group of polymer, -CH3 of the PNIPAM side chains, these water molecules must reorient being unable to form hydrogen bond with the non-polar groups in PNIPAM. This reorientation leads to formation of clathrate-like structures, this phenomenon is known as hydrophobic effect, results in decreased entropy upon mixing (negative ??S).1 When temperature is raised, the entropy term dominates the otherwise exothermic enthalpy of the hydrogen bonds formed between the polymer polar groups and water molecules that is the initial driving force for dissolution. Once the free energy change (??G) becomes positive upon mixing, the consequence is phase separation above a LCST as seen in the case of PNIPAM.1 If the concentration of th e PNIPAM is high enough, this replacement of PNIPAM-water contacts with PNIPAM-PNIPAM and water-water contacts is manifested by precipitation.1 In addition to the temperature???s inducing the collapse of the polymer chain, PNIPAM is insoluble in a proper mixture of water and methanol, despite both water and methanol being good solvents for PNIPAM at low temperature.1 The reentrant coil-to-globule-to-coil transition of PNIPAM takes place in a water/methanol mixture with an increase in the methanol content at room temperature. However, the mechanism of this transition is still not well established. It is believed that the transition is implicative to the solvation effect. Two potential mechanisms have been proposed. One suggested that the transition should be induced by the preferential adsorption of methanol molecules on PNIPAM. However, Theoretical calculations done by Pang et. al. demonstrate that water is as stable as methanol for staying in the vicinity of PNIPAM.5 The others ascribed it to the formation of water/methanol clusters. In addition to water/methanol clusters, pure water/water and methanol/methanol clu sters can also be formed in their mixtures and may affect the conformational change of polymer chain. MD simulation techniques can be used to evaluate the various hydrogen bonding interactions between methanol-water and methanol-polymer and methanol-methanol and understand the lowering of LCST at atomistic level. We plan to use MD simulation techniques to understand the role of methanol in influencing the LCST of PNIPAM at atomistic level. To carry out these MD simulations, a simulation cell with ~30-mer of PNIPAM will be solvated with a mixture of water and methanol with different molar ratios. Simulations will be carried out at 260, 278, and 310K for 40ns. The simulated MD trajectories will be used to evaluate the various structural (e.g. radius of gyration (Rg), radial distribution functions (rdf)), and transport properties of water molecules.

Project description: Accuracy of the model and MD simulation results mainly depends upon the method of structure generation and force-field used for MD simulations.6 In this work we propose to use the Polymer consistent force field (PCFF) to understand the atomic scale role of methanol on the LCST of PNIPAM.7 The preliminary studies we carried out with PCFF on the PNIPAM-pure water systems predicted the LCST close to 305K, which is in good agreement with the experimentally observed value. A fully atomistic level polymer chain of PNIPMA with ~30 monomer units will be placed in a simulation cell with water/methanol mixtures. Solvated polymer chains will then be equilibrated using MD simulations technique. Methanol concentration will be varied from 1M to 80M. In the case of PNIPAM, our preliminary studies and results from the literature show that to observe any phase transition in these systems, simulation time length must be in the range of 30-50ns. Simulations will be con ducted at 260, 278, and 310K for 40ns. Structural and dynamical properties will be studied for both polymer and water/methanol mixtures by analyzing trajectories of MD simulations. Transport properties of water and methanol will be studied using Einstein relation.6 The structural evolution in all the polymer and water/methanol systems will be studied and compared with each other to study the structure of water, methanol and PNIPAM 30-mer at different temperatures. The computational requirements for the proposed study will be substantial. For the proposed calculations, to study the phase transition across the LCST simulations should be run for ~40ns. From preliminary results of the simulations, we carried out on the CNM???s cluster Carbon and observed a clear phase transition across the LCST, for polymer chains with 30 monomer units (572 atoms) in presence of 9,000 water molecules. This system with ~30,000 atoms required ~145 hrs of simulation time for 10ns on 96 cores. In the proposed work we plan to study, PNIPAM 30-mer polymer chains in presence of different molar ratios of water/methanol mixtures. Total number of atoms in the systems we plan to study can vary from ~66,000 to ~42,000. Table 1 lists the systems we plan to study in detail.

Table 1: System details that are planned to study

# of PNIPAM #of water #of methanol methanol mole monomer units molecules molecules fractions 30 200 11000 0.018 30 1000 10000 0.09 30 2000 9000 0.18 30 3000 8000 0.27 30 5500 5500 0.5 30 8000 3000 0.73

We plan to study 6 different concentrations of water/methanol system as listed in Table 1. All the systems will be studied at 260, 278 and 310K (Total number of simulations = 6 x 3 = 18). Each simulation will be run for ~40ns (total simulation time = 18 x 40 = 720ns).

The estimated time for this particular work to carry out the mentioned calculations would be ~800,000 core hours.

References: 1.H. G. Schild, Prog. Polym. Sci. 1992, 17,163-249. 2. D. Schmaljohann, Adv. Drug Del. Rev. 2006, 58(15), 1655-1670. 3. A.S. Hoffman, J. of Cont. Rel. 1987, 6(1), 297-305. 4. H. Du, R. Wickramasinghe, and X. Qian, J. Phys. Chem. B 2010, 114, 16594-16604. 5. H. Y. J. Pang and R. Cheng, Journal of Physical Chemistry B, 2010, 114, 7429 - 7438. 6. M.P. Allen, D. J. Tildesley, Computer Simulations of Liquid, Clarendon Press, Oxford, 1987. 7. Accelrys, Inc. Cerius2 and Discover (programs) and Discover User Guide, version 96.0/4.0.0; Molecular Simulations, Inc.: San Diego, CA, 1996.

Project URL: Requested allocation: 800,000 Justification: To study the phase transition across the LCST in the case of single PNIPAM chain, simulations should be carried out for ~50ns. From preliminary results of the simulations we carried out on the CNM???s cluster Carbon, we observed a clear phase transition across the LCST, for polymer chains with 30 monomer units (572 atoms) in presence of 9,000 water molecules. This system with ~30,000 atoms required ~145 hrs of simulation time for 10ns on 96 cores.

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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