Recent Changes

Thursday, June 28

  1. page home edited Welcome to the Official Wikispace for theKavli Institute for Theoretical Physics programPhysical Pr…
    Welcome to the Official Wikispace for theKavli Institute for Theoretical Physics programPhysical Principles of Multiscale Modeling, Analysis and Simulation in Soft Condensed MatterApril 2 - June 29, 2012Coordinators: Paul Atzberger, Kurt Kremer, Mark Robbins
    ...
    Chemistry, by permission.Need Help?
    XXXX has volunteered to be the wikimaster for our program. She can be reached within the wikispaces message system by sending to XXX or by regular email here, by phone at extension #NNNN, or in person in office #MMMM.
    permission.
    Getting started
    Learning to use this wiki is no harder than learning to use email. Briefly, to edit a page, simply click the Edit tab at the top of the page. To add a page, click on the New Page item at the top left. Every page has a discussion board associated with it. To peruse the comments or to add your thoughts, click the discussion tab on the top of any page.
    (view changes)
    10:03 am
  2. page Reference Material edited Here's a page to share important papers, review articles, relevant news, etc. Wrap-up Discuss…

    Here's a page to share important papers, review articles, relevant news, etc.
    Wrap-up Discussion
    Topics/Questions for discussion at 9:30 am on Thursday June 28: Please add your ideas below
    Our final discussion on Thursday will look at where we've been and where we should go. Please contribute your thoughts so we make sure to cover the complete gamut on Thursday.
    ...
    1 (Petros Koumoutsakos):Koumoutsakos)
    Identify 2-3 problems with multiple, strongly coupled interacting time and/or space and/or structure scales -
    Can these be used for benchmarking/common developments for multi scale algorithms ?
    ...
    How do I decide which type of thermostat to use for nonequilibrium problems ? How do I know I did it correctly ?
    How can we tell up front for which quantities a coarse grained model will give the right answer ? Is there a systematic way to tell ? Or only on a case by case basis ?
    ...
    2 (Joerg Rottler):Rottler)
    I would like to raise again the question of coarse-graining in time vs coarse-graining in space.
    What options do we have to go beyond the nanosecond regime of MD, and for which classes of
    ...
    Sophistication: Will our field be more and more strongly dominated by a handful of extremely sophisticated software packages that fewer and fewer people truly understand (compare e.g. to the current state of quantum chemistry)? Is this OK? Is this inevitable? If so, how would we minimize the obvious dangers that go along with such a trend?
    Tuning: The development of CG potentials can be automated if (and only if!) we have a straightforward target to optimize, e.g. match g(r), match forces, minimize the relative entropy. But often we have a lot of extra physical intuition about what our CG model should achieve or avoid, but this is not easily formalized or quantified. How do we account for this? How do we address growing expectations that CG models ought to be constructed using some sort of automatization?
    Abstract for talk by PeterAbstract-Peter Daivis, Tuesday,
    Tuesday,
    June 12:
    In this talk, I will discuss two examples of the fruitful relationship between molecular
    dynamics simulations and continuum physics. The first is fluid slip, which can be studied
    ...
    notes on temperature {temperature derivation.pdf}
    Subtopic discussion list:
    How1. How structure determines
    (Will Noid)
    Certain "bottom-up" approaches to deriving coarse-grained potentials are often classified as force-based or structure-based. In previous work, we demonstrated that force-based coarse-graining can be accomplished without force information via a generalization of the Yvon-Born-Green integral equation theory. In the upcoming talk, I will discuss our more recent efforts to understand the relationship between force- and structure-motivated coarse-graining approaches by (1) formulating force-based coarse-graining within an information theoretic framework in analogy to that previously developed by Shell for iterative structure-based approaches; and (2) demonstrating that mean forces provide a unifying framework for relating force- and structure-motivated coarse-graining approaches and for understanding how many-body correlations influence coarse-grained potentials.
    ...
    Mean forces and many-body correlations:
    The Role of Many-Body Correlations in Determining Potentials for Coarse-Grained Models of Equilibrium Structure
    Discussion session on "reaction2. Reaction coordinates, collective
    ...
    degrees of freedom"
    (suggested
    freedom
    Discussion session (suggested
    by Peter
    When describing a dynamical system on a coarse level one needs to know which degrees of freedom to keep, and which can be integrated out. This question is related to the problem of finding a reaction coordinate that describes a dynamical (rare event) process.
    In coarse graining an atomistic system one integrates out the fast and irrelevant degrees of freedom, that represent only noise, while keeping the slow (collective) degrees of freedom. Providing that there are no memory effects, the system can then in principle be described by a Langevin equation in the coarse grained collective variable, with an effective diffusion constant.
    ...
    In this discussion we would like to find out the relations between these two approaches, and what can we learn from both.
    This informal discussion will take place on Monday afternoon 14 May at 1:30 pm in the Auditorium.
    Representability3. Representability problems
    (Ard Louis)
    Here are is a paper that I will be discussion on Tuesday --
    ...
    Coarse-graining dynamics by telescoping down time-scales: comment for Faraday FD144
    I briefly review some concepts related to coarse-graining methods for the dynamics of soft matter systems and argue that such schemes will almost always need to telescope down the physical hierarchy of time-scales to a more compressed, but more computationally manageable, separation.
    Hybrid all-atom -4. Hybrid all-atom, coarse-grained models
    (suggested by Siewert-Jan Marrink)
    Simulations in which the most critical part of the system is treated at an all-atom (AA) level and the surrounding is
    ...
    degrees of freedom. Questions open for discussion are i) Does one need to fully reparameterize the cross interactions or can one base it on
    existing AA and CG force fields, ii) How does one treat the electrostatic coupling (most AA force fields have -partial- charges, most CG force fields do not), and iii) How to avoid artefacts due to the incompatibility of bead sizes, iv) ...... v) ... mcxxv) ... mcxxvi). (no more please).
    Nanoparticles5. Nanoparticles in Polymer
    References suggested by M. Rubinstein
    Diffusion of nanoparticles in melts: Brochard-Wyart, F.; de Gennes, P. G. Eur. Phys. J. E 2000, 1, 93–97.
    ...
    One of recent theoretical models of Tg-shift:
    A Microscopic Model for the Reinforcement and the Nonlinear Behavior of Filled Elastomers and Thermoplastic Elastomers (Payne and Mullins Effects) by Samy Merabia, Paul Sotta, and Didier R. Long, Macromolecules, 2008, 41 (21), 8252-8266.
    Coarse-Grained6. Coarse-Grained Polymer Simulation
    Andrew Jewett recommended software package for text-manipulation tool for constructing LAMMPS simulation input files. (It can also be used to generate input for other molecular dynamics simulation software.)
    http://moltemplate.org
    (view changes)
    10:01 am

Wednesday, June 27

  1. page Social Activities edited ... Gary Grest (car + can take 2) Dvora Perahia Masao Doi (don't have car, but could take the b…
    ...
    Gary Grest (car + can take 2)
    Dvora Perahia
    Masao Doi (don't have car, but could take the bus)
    Group Dinner, Wednesday, June 20, 6:00pm
    I couldn't get reservations for tomorrow, so I've booked next week at the Boathouse.
    ...
    Boathouse at Hendry's Beach
    2981 Cliff Drive Santa Barbara, CA 93109
    805-898-2628 begin_of_the_skype_highlighting {skype-ie-addon-data://res/numbers_button_skype_logo.png} 無料 805-898-2628 end_of_the_skype_highlighting begin_of_the_skype_highlighting {skype-ie-addon-data://res/numbers_button_skype_logo.png}
    The menu is at http://www.sbfishhouse.com/boathouse/
    It's located right on a beach and you may want to plan time for a walk before or after the dinner.
    ...
    Mexican Restaurant
    600 N. Milpas, Santa Barbara, CA, 93103
    Work(805) 564-2626 begin_of_the_skype_highlighting {skype-ie-addon-data://res/numbers_button_skype_logo.png} 無料 (805) 564-2626 end_of_the_skype_highlighting begin_of_the_skype_highlighting {skype-ie-addon-data://res/numbers_button_skype_logo.png}
    http://www.menuclub.com/californiarestaurantguide/santabarbararestaurants/losagavesrestaurant-25334.php
    We'll need to go by car. Please indicate whether you can drive. If you can't, sign up under someone who can.
    ...
    6980 Market Place Drive, Goleta, CA
    Camino Real Marketplace
    (805) 968-2810 begin_of_the_skype_highlighting {skype-ie-addon-data://res/numbers_button_skype_logo.png} 無料 (805) 968-2810 end_of_the_skype_highlighting begin_of_the_skype_highlighting {skype-ie-addon-data://res/numbers_button_skype_logo.png}
    Easy to reach in Goleta on the corner of Storke and Hollister.
    Please sign up here up to 5 pm, May 30,(I have to call in the afternoon for a table):
    ...
    La Playa Azul Cafe Mexican / Seafood Restaurant
    914 Santa Barbara St., Santa Barbara, CA, 93101
    (805) 966-2860 begin_of_the_skype_highlighting {skype-ie-addon-data://res/numbers_button_skype_logo.png} 無料 (805) 966-2860 end_of_the_skype_highlighting begin_of_the_skype_highlighting {skype-ie-addon-data://res/numbers_button_skype_logo.png}
    Michael Rubinstein (have a car, can take 3+ people)
    Gary Grest (have a car, can take 2 people)
    ...
    6980 Market Place Drive, Goleta, CA
    Camino Real Marketplace
    (805) 968-2810 begin_of_the_skype_highlighting {skype-ie-addon-data://res/numbers_button_skype_logo.png} 無料 (805) 968-2810 end_of_the_skype_highlighting begin_of_the_skype_highlighting {skype-ie-addon-data://res/numbers_button_skype_logo.png}
    Easy to reach in Goleta on the corner of Storke and Hollister.
    Please sign up here up to 5 pm, May 10,(I have to call in the afternoon for a table):
    ...
    6920 Market Place Drive, Goleta, CA
    Camino Real Marketplace
    (805-685-7300 begin_of_the_skype_highlighting {skype-ie-addon-data://res/numbers_button_skype_logo.png} 無料 805-685-7300 end_of_the_skype_highlighting begin_of_the_skype_highlighting {skype-ie-addon-data://res/numbers_button_skype_logo.png}
    Easy to reach in Goleta on the corner of Storke and Hollister.
    Please sign up here up to 4pm, May 2,(I have to call in the afternoon for a table):
    ...
    6980 Market Place Drive, Goleta, CA
    Camino Real Marketplace
    (805) 968-2810 begin_of_the_skype_highlighting {skype-ie-addon-data://res/numbers_button_skype_logo.png} 無料 (805) 968-2810 end_of_the_skype_highlighting begin_of_the_skype_highlighting {skype-ie-addon-data://res/numbers_button_skype_logo.png}
    Easy to reach in Goleta on the corner of Storke and Hollister.
    Please sign up here up to 4pm, April 25,(I have to call in the afternoon for a table):
    (view changes)
    11:32 am
  2. page Reference Material edited ... Mixtures: In an N-component system we have O(N2) cross-interactions. This becomes a severe cro…
    ...
    Mixtures: In an N-component system we have O(N2) cross-interactions. This becomes a severe cross-parametrization problem if we wish to construct coarse grained potentials from the bottom up. Do we need to follow a different strategy here? (Compare how MARTINI, which is parametrized on mixing properties, aims to address this problem!)
    Successes: What are the big breakthroughs we have already achieved, especially in the light of existing expectations harbored outside of our community (which we presumably at some point in the past have raised)? Has coarse graining delivered or fallen short of its promises? Has this consequences for how we as a community advertise its merits?
    ...
    of quantum chemistry).chemistry)? Is this
    ...
    automated if (and only if!) we have
    Abstract for talk by Peter Daivis, Tuesday, June 12:
    In this talk, I will discuss two examples of the fruitful relationship between molecular
    (view changes)
    10:47 am
  3. page Reference Material edited ... Representability: How can we know ahead of time which observables are correctly represented in…
    ...
    Representability: How can we know ahead of time which observables are correctly represented in a coarse grained model? And if we know they will not, can we at least know ahead of time how big the systematic error might be: ten percent? factor of two? four orders of magnitude? Can we put a (systematic) error bar on multiscaling? If not, what does it mean to "predict" something?
    Target: What are the right things we should calculate using multiscaling? Is the aim really to get accurate numbers? Does the answer to that question depend on whether we're scientists or engineers? What should we specifically strive for if we're physicists?
    ...
    be that systematic coarse graining
    ...
    detail of ana coarse grained interaction right?
    Preconditions: How strongly does the success of scale-bridging depend on our pre-existing understanding of the physics on larger scales, or even on its universality? For instance, polymer science is awesome for physicists, because there's so much universality in it. Hence, systematic course graining better aims at the non-universal prefactors. If these can be extracted from fairly local physics, coarse graining will work very well, but can we expect such a nice scenario for other systems that don't exhibit a comparable degree of universality (e.g. proteins or composites)? This conceivably boils down to the question: For which type of systems is multiscaling a promising strategy?
    Mixtures: In an N-component system we have O(N2) cross-interactions. This becomes a severe cross-parametrization problem if we wish to construct coarse grained potentials from the bottom up. Do we need to follow a different strategy here? (Compare how MARTINI, which is parametrized on mixing properties, aims to address this problem!)
    (view changes)
    10:44 am
  4. page Reference Material edited ... Suggestion 2 (Joerg Rottler): I would like to raise again the question of coarse-graining in …
    ...
    Suggestion 2 (Joerg Rottler):
    I would like to raise again the question of coarse-graining in time vs coarse-graining in space.
    ...
    classes of
    problems

    problems
    do these
    ...
    to the
    experimental time scales and how do we make sure that we have not missed any "rare events"
    that would change the physics?
    Suggestions 3 (Markus Deserno)
    I have picked a set of issues I personally find interesting and have phrased associated challenges as questions. I have entirely restricted to equilibrium, since I feel the number of fundamental questions we do not yet understand is plenty.
    Representability: How can we know ahead of time which observables are correctly represented in a coarse grained model? And if we know they will not, can we at least know ahead of time how big the systematic error might be: ten percent? factor of two? four orders of magnitude? Can we put a (systematic) error bar on multiscaling? If not, what does it mean to "predict" something?
    Target: What are the right things we should calculate using multiscaling? Is the aim really to get accurate numbers? Does the answer to that question depend on whether we're scientists or engineers? What should we specifically strive for if we're physicists?
    Minimal models: Coarse graining might teach us about the minimal physical input for a given phenomenon of interest. If we have managed to build an "irreducible model", most likely its enthalpic and entropic contributions balance in a way that resembles the real situation. Could it be that coarse graining often works because it assures that this balance is achieved? If so, is there a genuine and quantifiable benefit of additionally getting every single detail of an interaction right?
    Preconditions: How strongly does the success of scale-bridging depend on our pre-existing understanding of the physics on larger scales, or even on its universality? For instance, polymer science is awesome for physicists, because there's so much universality in it. Hence, systematic course graining better aims at the non-universal prefactors. If these can be extracted from fairly local physics, coarse graining will work very well, but can we expect such a nice scenario for other systems that don't exhibit a comparable degree of universality (e.g. proteins or composites)? This conceivably boils down to the question: For which type of systems is multiscaling a promising strategy?
    Mixtures: In an N-component system we have O(N2) cross-interactions. This becomes a severe cross-parametrization problem if we wish to construct coarse grained potentials from the bottom up. Do we need to follow a different strategy here? (Compare how MARTINI, which is parametrized on mixing properties, aims to address this problem!)
    Successes: What are the big breakthroughs we have already achieved, especially in the light of existing expectations harbored outside of our community (which we presumably at some point in the past have raised)? Has coarse graining delivered or fallen short of its promises? Has this consequences for how we as a community advertise its merits?
    Sophistication: Will our field be more and more strongly dominated by a handful of extremely sophisticated software packages that fewer and fewer people truly understand (compare e.g. to the current state of quantum chemistry). Is this OK? Is this inevitable? If so, how would we minimize the obvious dangers that go along with such a trend?
    Tuning: The development of CG potentials can be automated if we have a straightforward target to optimize, e.g. match g(r), match forces, minimize the relative entropy. But often we have a lot of extra physical intuition about what our CG model should achieve or avoid, but this is not easily formalized or quantified. How do we account for this? How do we address growing expectations that CG models ought to be constructed using some sort of automatization?

    Abstract for talk by Peter Daivis, Tuesday, June 12:
    In this talk, I will discuss two examples of the fruitful relationship between molecular
    (view changes)
    10:42 am
  5. page Reference Material edited ... How do I decide which type of thermostat to use for nonequilibrium problems ? How do I know I …
    ...
    How do I decide which type of thermostat to use for nonequilibrium problems ? How do I know I did it correctly ?
    How can we tell up front for which quantities a coarse grained model will give the right answer ? Is there a systematic way to tell ? Or only on a case by case basis ?
    Suggestion 2 (Joerg Rottler):
    I would like to raise again the question of coarse-graining in time vs coarse-graining in space.
    What options do we have to go beyond the nanosecond regime of MD, and for which classes of
    problems do these methods work? If we do nonequilibrium MD, how do we extrapolate to the
    experimental time scales and how do we make sure that we have not missed any "rare events"
    that would change the physics?

    Abstract for talk by Peter Daivis, Tuesday, June 12:
    In this talk, I will discuss two examples of the fruitful relationship between molecular
    (view changes)
    9:59 am
  6. page Social Activities edited ... Karin Dahmen (no car) Karsten Kreis (no car) Gary Grest (car + can take 2) Dvora Perahia …
    ...
    Karin Dahmen (no car)
    Karsten Kreis (no car)
    Gary Grest (car + can take 2)
    Dvora Perahia

    Group Dinner, Wednesday, June 20, 6:00pm
    I couldn't get reservations for tomorrow, so I've booked next week at the Boathouse.
    (view changes)
    9:00 am

Tuesday, June 26

  1. page Reference Material edited ... can I have an autofix for the times when force matching goes wrong? what if I want to guarant…
    ...
    can I have an autofix for the times when force matching goes wrong?
    what if I want to guarantee I get the same chemical potential as my atomistic model?
    How do I decide which type of thermostat to use for nonequilibrium problems ? How do I know I did it correctly ?
    How can we tell up front for which quantities a coarse grained model will give the right answer ? Is there a systematic way to tell ? Or only on a case by case basis ?

    Abstract for talk by Peter Daivis, Tuesday, June 12:
    In this talk, I will discuss two examples of the fruitful relationship between molecular
    (view changes)
    11:41 pm

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