Biological Physics (FIM 3404)

Schedule

Please find here our schedule for year 2018

Textbook

As last year, we will base our tour through papers around issues outlined in the textbook Physical Biology of the Cell described online here.

Measuring standard

As suggested by the book we are heavely E.coli centric. For the over-biological approach consult here . For useful biological numbers check here .

Lecture Slides

Part I. Facts of Life: [Lecture 1 (7/3/2018)] | [Lecture 2 (12/3/2018)] | [Lecture 3 (14/3/2018)]
Part II. Life at rest: [Lecture 4 (19/3/2018)] | [Lecture 5 (21/3/2018)] | [Lecture 6 (26/3/2018)] | [Lecture 7 (2/4/2018)] | [Lecture 8 (4/4/2018)] | [Lecture 9 (9/4/2018)] | [Lecture 10 (11/4/2018)]
Part III. Life in Motion:

Papers

1.- Joselyn Valenzuela Ferry will present [Lovelock life detection test] Nature Vol. 207, No. 4997, pp. 568-570, August 7, 1965 Along with Lovelocks toy planetary model [Daisyworld]
2.- [Fonatana's algoritmic chemistry] PNAS January 18, 1994. 91 (2) 757-761
3.- [Maturana and Varela autopoiesis] Biosystems Volume 5, Issue 4, May 1974, Pages 187-196
4.- [Smith and Morowitz. Universality of intermediary metabolism] PNAS September 7, 2004. 101 (36) 13168-13173
5.- Pablo Galaz Davison will present [Dunker and Obradovic. The protein trinity-linking function and dissorder] Nat Biotechnol. 2001 Sep;19(9):805-6.
6.- Juan Manuel Gonzalez Brantes will present [Lim et al. Red blood cells membrane mechanics] PNAS December 24, 2002. 99 (26) 16766-16769
7.- [Si et al. Growth and form under mechanical compression] Scientific Reports volume 5, Article number: 11367 (2015)
8.- Francisca Palacios will present [Mittal et al. E. coli clusters formed by chemotactic aggregation] PNAS November 11, 2003. 100 (23) 13259-13263
9.- [England et al. Statistical physics of adaptation] Phys. Rev. X 6, 021036 June 16, 2016
10.- [BTW Self-Organized Criticality] Phys. Rev. Lett. 59, 381 July 27, 1987
11.- [Phil W Anderson, More is Different] Science August 4, 1972
12.- [Christopher Langton, Langton Self-replicating Automata: Loops] Physica D: Nonlinear Phenomena January 1984
13.- [Wang et al. Mother Machine] Current Biology June 22, 2010, Pages 1099-1103
14.- [Geoffrey West, Scaling laws in Biology] Science April 4, 1997
15.- [Stephen Wolfram, NKS]
16.- Alfredo L'Homme will present [Stuart Kauffman, Origin of Order] Spin glasses and biology, 1992
17.- Jorge Riveros Vergara will present [Predictive Behavior Within Microbial Genetic Networks ] Science May 8, 2008
18.- Francisca Saez will present [Entropy-driven spatial organization of highly confined polymers: Lessons for the bacterial chromosome PNAS August 15, 2006. 103 (33) 12388-12393
19.- [Sanchez et al. Spontaneous motion in hierarchically assembled active matter] Nature, November 15, 2012
20.- [Chen et al. Weak synchronization and large-scale collective oscillation in dense bacterial suspensions] Nature, February 9, 2017
21.- [Antebi et al. Combinatorial Signal Perception in the BMP Pathway] Cell, September 7, 2017
22.- [Attanasi et al. Information transfer and behavioral inertia in starling flocks] Nature Physics volume 10, 2014

Supplementary Materials

Here you can find links to interesting talks and more mentioned during lectures:

Island Biogeography of Microbes with Jessica Green

The scaling laws of life with Geoffrey West

Computing a theory of knowledge

A link to the Active Matter team @ UChile

A blog post breaking down Phil Andersons example of broken symmetry in "More is Different"

The science of sync.

Entropic gravity mentioned during lecture (21/3/18)

Stefan Hell, Nobel Prize in Chemistry (2014) for super-resolved flurorescence microscopy.



The paper trail of long-distance communication in bacteria

1.-[Metabolic co-dependence gives rise to collective oscillations within biofilms.] Along with SI including videos.

2.-[Ion channels enable electrical communication in bacterial communities.] Along with SI including videos.

3.-[Coupling between distant biofilms and emergence of nutrient time-sharing.] Along with SI including videos.

4.-[Species-Independent Attraction to Biofilms through Electrical Signaling.] Along with SI including videos.



Pilot wave dynamics of silicon droplets, video

Materials discussed in class (15/4/18):  



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