Computational anatomy and diffeomorphometry: A dynamical systems model of neuroanatomy in the soft condensed matter continuum

The renormalization group (RG) method developed by Ken Wilson more than four decades ago has revolutionized the way we think about problems involving a broad range of energy scales such as phase transitions, turbulence, continuum limits and bifurcations in dynamical systems. The Theme Issue provides articles reviewing recent progress made using the RG method in atomic, condensed matter, nuclear and particle physics. In the following, we introduce these articles in a way that emphasizes common themes and the universal aspects of the method.

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2nd International Workshop on Soft Condensed Matter Physics and Biological Systems (SMPPMM 2010)

Applied Rheology ◽

10.1515/arh-2010-0005 ◽

2010 ◽

Vol 20 (3) ◽

pp. 176-176

Author(s):

Benhamou Mabrouk

Keyword(s):

Condensed Matter ◽

International Workshop ◽

Biological Systems ◽

Condensed Matter Physics ◽

Soft Condensed Matter

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A computational framework for finding parameter sets associated with chaotic dynamics

In Silico Biology ◽

10.3233/isb-200476 ◽

2021 ◽

pp. 1-11

Author(s):

S. Koshy-Chenthittayil ◽

E. Dimitrova ◽

E.W. Jenkins ◽

B.C. Dean

Keyword(s):

Experimental Data ◽

Dynamical Systems ◽

Lyapunov Exponents ◽

Parameter Space ◽

Chaotic Dynamics ◽

Chaotic Behavior ◽

Computational Framework ◽

Independent Variables ◽

Systems Model ◽

Small Support

Many biological ecosystems exhibit chaotic behavior, demonstrated either analytically using parameter choices in an associated dynamical systems model or empirically through analysis of experimental data. In this paper, we use existing software tools (COPASI, R) to explore dynamical systems and uncover regions with positive Lyapunov exponents where thus chaos exists. We evaluate the ability of the software’s optimization algorithms to find these positive values with several dynamical systems used to model biological populations. The algorithms have been able to identify parameter sets which lead to positive Lyapunov exponents, even when those exponents lie in regions with small support. For one of the examined systems, we observed that positive Lyapunov exponents were not uncovered when executing a search over the parameter space with small spacings between values of the independent variables.

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Quantitative Ultrafast Spectroscopy and Microscopy of Traditional and Soft Condensed Matter

Applied Sciences ◽

10.3390/app8081317 ◽

2018 ◽

Vol 8 (8) ◽

pp. 1317

Author(s):

Adam Card ◽

Mohammad Mokim ◽

Feruz Ganikhanov

Keyword(s):

Condensed Matter ◽

Potassium Titanyl Phosphate ◽

Soft Condensed Matter ◽

Phonon Modes ◽

Third Order ◽

Unit Cells ◽

Coherent Optical Spectroscopy ◽

Series Of Experiments ◽

Tio6 Octahedron ◽

Better Than

We demonstrate and analyze a series of experiments in traditional and soft condensed matter using coherent optical spectroscopy and microscopy with ultrafast time resolution. We show the capabilities of resolving both real and imaginary parts of the third-order nonlinearity in the vicinity of Raman resonances from a medium probed within microscopic volumes with an equivalent spectral resolution of better than 0.1 cm−1. We can differentiate between vibrations of various types within unit cells of crystals, as well as perform targeted probes of areas within biological tissue. Vibrations within the TiO6 octahedron and the ones for the Ti-O-P intergroup were studied in potassium titanyl phosphate crystal to reveal a multiline structure within targeted phonon modes with closely spaced vibrations having distinctly different damping rates (~0.5 ps−1 versus ~1.1 ps−1). We also detected a 1.7–2.6 ps−1 decay of C-C stretching vibrations in fat tissue and compared that with the corresponding vibration in oil.

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