LIR Computational Physics Group

http://www.ingber.com/lir_computational_physics_group.html

Lester Ingber

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Please note that I regularly address short technical queries via email, at no charge. See http://www.ingber.com/ingber_terms.html

To facilitate collaboration with other researchers via the internet, I can offer a common platform described on which I am Principal Investigator (PI) of a National Science Foundation (NSF.gov) Extreme Science and Engineering Discovery Environment (XSEDE.org) supercomputer-resource grant, based on ideas as presented in a paper generated by the project
%A L. Ingber
%A M. Pappalepore
%A R.R. Stesiak
%J Journal of Theoretical Biology
%T Electroencephalographic field influence on calcium momentum waves
%V 343
%P 138-153
%D 2014
%O URL http://www.ingber.com/smni14_eeg_ca.pdf and http://dx.doi.org/10.1016/j.jtbi.2013.11.002
Slides of a brief presentation are at http://ingber.com/smni13_eeg_ca_lect.pptx and http://ingber.com/smni13_eeg_ca_lect.pdf

Reviews and XSEDE press releases on this work are at http://www.ingber.com/smni14_eeg_ca_JTB_reviews.txt

An invited paper in preparation is
%A L. Ingber
%T Influences on consciousness from multiple scales of neocortical interactions
%B Frontiers in Physiology/Biophysics: Non-chemical distant cellular interactions: experimental evidences, theoretical modeling, and physiological significance
%E M. Cifra
%E V. Salari
%E D. Fels
%E F. Scholkmann
%D 2014
%O Invited Paper. URL http://www.ingber.com/smni14_conscious_scales.pdf
Slides of a brief presentation are at http://ingber.com/smni14_conscious_scales_lect.pptx and http://ingber.com/smni14_conscious_scales_lect.pdf

This grant is for use of these resources for applications of computational physics as used in the above references, based on some projects related to those I have worked on previously. Work performed under an initial grant spanning 20 Feb 2013 - 19 Aug 2014 passed peer review for a second research grant spanning 1 Jul 2014 - 30 Jun 2015.

Note that this is a platform that gives opportunities in research collaboration for volunteers. Depending on your contributions, your rewards may be learning, producing new algorithms, acknowledgements, co-authorship, personal references that may help your career, etc.

If you are interested in collaborating on my XSEDE project, below are the steps I have volunteers use.

In all correspondence, please provide links instead of attachments whenever possible. If you cannot share individual files from Google Drive, Skydrive, Dropbox, etc., there are plenty of other similar free services.

Project: "Mind Over Matter"

"Mind Over Matter" is a stretch, but not inaccurate, context for this project. The logic is:

(1) A lot of what we consider "mind" is conscious attention to short-term memories, which can develop by (a) external stimuli directly, (b) internal long-term storage, (c) new ideas=memories developed in abstract regions of the brain, etc.

(2) It is now accepted by some to many neuroscientists, and confirmed by some experiments, that at least some such memories in (1) are actively processed by highly synchronized patterns of neuronal firings, with enough synchrony to be able to be easily measured by scalp EEG during activity of processing such patterns, e.g., P300 waves, etc. (E.g., see https://www.xsede.org/mechanism-of-short-term-memory and http://www.sdsc.edu/News%20Items/PR041414_short_term_memory.html .) These minicolumnar currents giving rise to measurable EEG also give rise to magnetic vector potentials A. The A fields have a logarithmic range insensitivity and are additive over larger distances than E or B fields.

(3) The recent JTB paper calculates the influence of such synchronous EEG at molecular scales of Ca2+ ionic waves, a process which is present in the body and brain, but particularly as astrocyte influences at synaptic gaps, thereby affecting background synaptic activity, which in turn can be synchronized by other processes to give rise to the large-scale activity discussed in (1). The Ca2+ wave have a duration of momentum p which is observed to be rather large.

(4) The recent paper connects the influence of (1) over (3) directly via a specific interaction, p+qA, where q for a Ca2+ ion = 2e, where e is the magnitude of the charge of an electron. The p+qA interaction is well established in both classical and quantum physics.

The direct p+qA influence of (1) over (3) can reasonably be discussed as a "mind over matter" process. E.g., just thinking about thinking can give rise to this effect.

(5) The JTB paper reports the use of MPI to parallelize code that fits EEG data to a model that includes the dynamic influence of a p+qA interaction on background synaptic activity, embedded in my Statistical Mechanics of Neocortical Interactions (SMNI) coded model, to assess the viability EEG activity influencing this interaction. This now provides a testbed for future models of such interactions.

Contact Me Via Email

Contact me with an email to ingber@alumni.caltech.edu so we can discuss whether you and the project would benefit from your membership. If this is agreed upon, then continue to the next steps.

Set Up An Account On XSEDE

(1) Set up your own account on http://www.xsede.org . Also, see https://www.xsede.org/using-xsede#step2 to set up a Portal Account. This all is is pretty straightforward. It will take a day or two until your registration is in the XSEDE system. Send me an email to ingber@alumni.caltech.edu to tell me the user name and email address you used to register.

(2) When I see your registered name and email in XSEDE, I can add you as a user to this project on xsede.org, which can take over a day for XSEDE to process. Currently we have accounts at different XSEDE sites. I will send you an email when this step is complete.

(3) I do due diligence on the activity in this group regularly. If you have not make any contact with me, or have not done any work on any of our xsede projects within the past month, I'll remove you from this xsede project. This will not affect your registration on xsede.org and you still can benefit from that.

I have to do this to be able to monitor the progress of these projects, and to know who to depend on for future progress. If you find that you have been removed, and feel I made an error in doing so, please just contact me by sending an email to ingber@alumni.caltech.edu so that I can consider putting you back into the project.

Possible Sub-Projects

The above-mentioned paper http://www.ingber.com/smni14_eeg_ca.pdf discusses several sub-projects that would be useful to the overall project, e.g., including developing models of astrocyte-neuron Ca2+ influences on synchronous background synaptic activity, developing models to test for prolonged quantum coherence of specific Ca2+ waves in astrocyte-neuron interactions due to repeated generation/collisions among these ions, etc.

A particular computational-physics sub-project that would be useful across many disciplines is to extend an existing code PATHTREE to multiple variables and to parallelize it. It's importance for this project is discussed in the above-mentioned paper http://www.ingber.com/smni14_eeg_ca.pdf

A description of the code is in:


%A L. Ingber
%A C. Chen
%A R.P. Mondescu
%A D. Muzzall
%A M. Renedo
%T Probability tree algorithm for general diffusion processes
%J Physical Review E
%V 64
%N 5
%P 056702-056707
%D 2001
%O URL http://www.ingber.com/path01_pathtree.pdf

The extension to multiple variables has been done in PATHINT which is mentioned in that paper, and described in some other papers, e.g.,


%A L. Ingber
%A P.L. Nunez
%T Statistical mechanics of neocortical interactions: High resolution path-integral calculation of short-term memory
%J Physical Review E
%V 51
%N 5
%P 5074-5083
%D 1995
%O URL http://www.ingber.com/smni95_stm.pdf


%A L. Ingber
%A R. Srinivasan
%A P.L. Nunez
%T Path-integral evolution of chaos embedded in noise: Duffing neocortical analog
%J Mathematical Computer Modelling
%V 23
%N 3
%P 43-53
%D 1996
%O URL http://www.ingber.com/path96_duffing.pdf


%A L. Ingber
%A J.K. Wilson
%T Statistical mechanics of financial markets: Exponential modifications to Black-Scholes
%J Mathematical Computer Modelling
%V 31
%N 8/9
%P 167-192
%D 2000
%O URL http://www.ingber.com/markets00_exp.pdf

The PATHINT code looks a bit clumsy, but it is general for N variables, but so slow I have only used it in some papers for N = 2.

The codes already are in vanilla C, so they run on any platform. OpenMP or MPI would be fine to consider for parallelization.

In order to process quantum distributions, even after "Wick-rotation" of time, there still would be complex variables in the drift due to the magnetic vector potential. The code needs to be modified to have the relevant variables be defined as Complex.

Note that both PATHTREE and PATHINT are quite generic across many disciplines, and would be a welcome public algorithm. These codes would be published under the modified BSD licenses, as I have done for my Adaptive Simulated Annealing (ASA) code, which has added OpenMP parallelization in this project.

Thanks.

Lester


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Lester Ingber <lester@ingber.com>
Copyright © 2013-2014 Lester Ingber. All Rights Reserved.

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