complexsystems

Complex Systems

http://code.google.com/p/dsmts/ Discrete Stochastic Models Test Suite

http://xstructure.inr.ac.ru/index.html search in Arxiv.org

http://www.asmda.net/chaos2008/

Cosma Rohilla Shalizi :

http://www.cscs.umich.edu/~crshalizi/research

http://www.stat.cmu.edu/~cshalizi/462/syllabus.html

Institute Of Nonlinear Science, San Diego http://inls.ucsd.edu

PERSONAL PAGES

http://chaos.phys.msu.ru/loskutov/PDF/ Loskutov

http://www.weizmann.ac.il/home/fnfal Gregory Falkovich

Lev Tsimring http://inls.ucsd.edu/~lev

Misha Chertkov http://cnls.lanl.gov/~chertkov

Solomon Sorin http://shum.huji.ac.il/~sorin

Arkady Pikovsky http://www.scholarpedia.org/article/User:Pikovsky

http://www.stat.physik.uni-potsdam.de/~pikovsky

http://www.menem.com/~ilya/wiki/index.php/Ilya_Nemenman

http://ocw.mit.edu/OcwWeb/Mathematics/18-385JFall-2004/CourseHome/index.htm

http://ocw.mit.edu/OcwWeb/Earth--Atmospheric--and-Planetary-Sciences/12-006JFall-2006/CourseHome/index.htm

http://ocw.mit.edu/OcwWeb/Physics/8-592JSpring-2005/LectureNotes/index.htm

http://www.math.sunysb.edu/dynamics/

http://www.dynamical-systems.org/

http://chaos.ssu.runnet.ru Saratov Anishenko

http://www.ulsu.ru/staff/homepages/uchaikin/ Uchaikin

http://www.wel.atr.jp/nos/ddap5/

http://www.jst.go.jp/erato/project/kcs_P/kcs_P.html ERATO

http://www.jst.go.jp/erato/project/ahs_P/ahs_P.html

Local files:

Methods And Techniques for the Complex Systems

Power Law Distribution

Wikipedia / Scholarpedia Links:

http://en.wikipedia.org/wiki/It%C5%8D_calculus Ito calculus

http://en.wikipedia.org/wiki/Stochastic_Calculus

http://en.wikipedia.org/wiki/Stratonovich_integral

http://en.wikipedia.org/wiki/Stochastic_modeling

http://www.scholarpedia.org/article/Stochastic_resonance

http://en.wikipedia.org/wiki/Stochastic_resonance

http://en.wikipedia.org/wiki/Master_equation

http://en.wikipedia.org/wiki/Gillespie_algorithm

http://qwiki.stanford.edu/wiki/Recurrent_Stochastic_Process

http://qwiki.stanford.edu/wiki/Simulating_an_Ornstein-Uhlenbeck_Process

Dynamical Systems

http://www.scholarpedia.org/article/Stochastic_dynamical_systems

http://en.wikipedia.org/wiki/Dynamical_systems

http://www.scholarpedia.org/article/Encyclopedia_of_dynamical_systems

http://brain.cc.kogakuin.ac.jp/~kanamaru/Chaos/e

http://www.maths.qmul.ac.uk/~klages/teaching/ltcc_ads

http://www.wisdom.weizmann.ac.il/~vered/dynsys07.html

http://chaosbook.org/

Molecular Dynamics software packages

GROMACS (Lindahl et al., 2001; van der Spoel et al., 2005)

CHARMM (MacKerell et al., 1998),

AMBER (Case et al., 2006) and NAMD (Phillips et al., 2005).

Each of these packages consists of a complex force field to describe interactions between the particles in a system and numerical algorithms to solve

Newton’s second law based on the forces predicted by these fields.

http://homepages.nyu.edu/~mt33/

http://www.stonybrook.edu/geosciences/people/faculty/oganov/oganov.html

Random Matrix http://en.wikipedia.org/wiki/Random_matrix_theory

Random Walk http://en.wikipedia.org/wiki/Quantum_random_walk

http://accu.org/index.php/journals/1494

The "arcsine distribution" as applied to random walks is as follows:

Let X₁, X₂, ... be independent random variables which are each +1 with probability 1/2 and -1 with probability 1/2. Let S_n = X₁ + X₂ + ... + X_n. Consider the sequence (S₁, ..., S_2n) -- now, what's the probability that the last zero in this sequence comes between time 2an and 2bn? It turns out that as n approaches infinity, this probability approaches

and in particular, the last zero is surprisingly likely to be near 0 or 2n, and surprisingly unlikely to be somewhere in the middle.

Biochemical systems, negative feedback, Goodwin model

http://en.wikipedia.org/wiki/Gene_regulatory_network

http://en.wikipedia.org/wiki/Signal_transduction

http://sbml.org System Biology Markup Language

http://sbml.org/SBML_Software_Guide/SBML_Software_Matrix

http://www.icsb-2007.org/tutorials/index.html

http://www.ricam.oeaw.ac.at/people/page/jameslu/Teaching/

http://ocw.mit.edu/OcwWeb/Physics/8-591JFall2004/Readings/index.htm

http://smt.nichd.nih.gov/bezrukov.htm

Control Theory in Biology

Tsimring

http://basil2.math.uwaterloo.ca/~bingalls

http://basil2.math.uwaterloo.ca/~bingalls/ICSB03tutorial

Stochastic resonance

http://en.wikipedia.org/wiki/Stochastic_resonance

http://www.scholarpedia.org/article/Stochastic_resonance

The N.i.P.S. Laboratory is proud to announce event: the International Conference STOCHASTIC RESONANCE 2008, to be held in Perugia on Aug. 17-21, 2008.

http://www.fisica.unipg.it/gammaitoni/sr/index.html

http://chaos1.la.asu.edu/~yclai/pub.html

Chimera states: the natural link between coherence and incoherenc

http://igorivanov.blogspot.com/2008/02/blog-post_03.html

Omel'chenko OE, Maistrenko YL Popovych

http://xstructure.inr.ac.ru/x-bin/searchI3.py?level=2&index1=-301927&Title=stochastic&Author=&time_p=-&Year=&view_type=list+of+articles&Key_sp=&Sort=Citation+number&skip=0

Kuramoto

Local file: Kuramoto

http://www.ncbi.nlm.nih.gov/sites/entrez?tool=QuerySuggestion&cmd=search&db=pmc&term=Kuramoto%20noise%20cell%20synchronization

http://adsabs.harvard.edu/cgi-bin/nph-abs_connect?bibcode=2004APS..MARY18008T&return_req=no_params&selfeedback=1&use_title=YES&use_kwds=YES&return_req=feedback

Molecular Motors http://en.wikipedia.org/wiki/Brownian_motor

http://xstructure.inr.ac.ru/x-bin/theme2.py?arxiv=cond-mat&level=2&index1=57

http://www.ks.uiuc.edu/Research/helicase/

http://lenta.ru/news/2007/12/25/nanomotor/

http://lenta.ru/news/2008/12/16/nanomotor/

http://www.newscientist.com/article/mg20126884.300-nanobot-lets-dna-legs-do-the-walking.html?DCMP=OTC-rss&nsref=online-news

http://www.c3.lanl.gov/cb/index.shtml

http://monet.physik.unibas.ch/~elmer/bm/

http://ocw.mit.edu/OcwWeb/Physics/8-592JSpring-2005/LectureNotes/index.htm

Biological Networks

It has been widely reported that biological networks are robust against perturbations such as mutations. On the contrary, it has also been known that biological networks are often fragile against unexpected mutations ...

http://bioinformatics.oxfordjournals.org/cgi/reprint/24/7/987

http://bioinformatics.oxfordjournals.org/cgi/reprint/24/6/833

http://www.biomedcentral.com/bmcbioinformatics/

Magazine: Stochastic Processes and their Applications http://www.sciencedirect.com/science/journal/03044149

http://www.ped.fas.harvard.edu/people/faculty/ Martin Novak

Synchronization in complex networks

http://arxiv.org/PS_cache/arxiv/pdf/0805/0805.2976v2.pdf

Boltzmann machine http://www.scholarpedia.org/article/Boltzmann_machine

Levy process

http://en.wikipedia.org/wiki/L%C3%A9vy_process