Computations in Science Seminars
Oct 2018
3
Wed 12:15
Marija Vucelja, University of Virginia
e-mail:
Host: Arvind Murugan ()
Organizer: Zhiyue Lu ()
Adaptation of a bacterial population and the adaptive immune system of bacteria with CRISPR

The CRISPR (clustered regularly interspaced short palindromic repeats) mechanism allows bacteria to defend adaptively against phages and other invading genomic material. The CRISPR machinery acquires short genomic sequences from the "invaders" and in this way builds up a memory of past infections. With a new encounter of an invading sequence, this memory is accessed, and in a successful outcome, the invader is neutralized. I will introduce a population dynamics model where immunity can be both acquired and lost. I will describe the predictions of this model and suggest experiments.

Adaptation, where a population evolves increasing fitness in a fixed environment is often thought of as a hill climbing process on a fitness landscape. With a fi nite genome, such a process eventually leads the population to a fitness peak, at which point fitness can no longer increase through individual beneficial mutations. Instead, the ruggedness of typical landscapes due to epistasis between genes or DNA sites suggests that the accumulation of multiple mutations can allow the population to continue increasing in fitness. By using a spin-glass type model for the fitness function that takes into account microscopic epistasis, we find that hopping between metastable states can mechanistically and robustly give rise to a slow, logarithmic average fitness trajectory.

Oct 2018
10
Wed 12:15
Shinsei Ryu, University of Chicago
e-mail:
Host: William Irvine ()
Oct 2018
17
Wed 12:15
OPEN
Oct 2018
24
Wed 12:15
Jörn Dunkel, MIT
e-mail:
Host: William Irvine ()
Oct 2018
31
Wed 12:15
Timothy C. Berkelbach, University of Chicago
e-mail:
Host: Arvind Murugan ()
Nov 2018
7
Wed 12:15
Brad Marston, Brown University
e-mail:
Host: William Irvine ()
Nov 2018
14
Wed 12:15
Oni Basu, University of Chicago
e-mail:
Host: Arvind Murugan ()
Nov 2018
28
Wed 12:15
Felice Frankel, MIT
e-mail:
Host: Sid Nagel ()
Dec 2018
5
Wed 12:15
David Lubensky, University of Michigan
e-mail:
Host: Arvind Murugan ()
Dec 2018
12
Wed 12:15
Chiara Daraio, Caltech
e-mail:
Host: William Irvine ()
Jan 2019
9
Wed 12:15
OPEN
Jan 2019
16
Wed 12:15
Margaret Gardel, University of Chicago
e-mail:
Host: Arvind Murugan ()
Jan 2019
23
Wed 12:15
OPEN
Jan 2019
30
Wed 12:15
OPEN
Feb 2019
6
Wed 12:15
OPEN
Feb 2019
13
Wed 12:15
OPEN
Feb 2019
20
Wed 12:15
Greg Voth, Wesleyan University
e-mail:
Host: William Irvine ()
Feb 2019
27
Wed 12:15
OPEN
Mar 2019
13
Wed 12:15
OPEN
Mar 2019
20
Wed 12:15
OPEN
Mar 2019
27
Wed 12:15
OPEN
Apr 2019
3
Wed 12:15
Greg Bewley, Cornell University
e-mail:
Host: William Irvine ()
Apr 2019
10
Wed 12:15
Oskar Hallatschek, UC Berkeley
e-mail:
Host: Arvind Murugan ()
Apr 2019
17
Wed 12:15
Nikta Fakhri, MIT
e-mail:
Apr 2019
24
Wed 12:15
Detlef Lohse, University of Twente
e-mail:
Host: William Irvine ()
May 2019
1
Wed 12:15
Pankaj Mehta, Boston University
e-mail:
Host: Stefano Allesina
May 2019
8
Wed 12:15
Thierry Emonet, Yale University
e-mail:
Host: Arvind Murugan ()
May 2019
15
Wed 12:15
David Lentik, Stanford
e-mail:
Host: William Irvine ()
May 2019
22
Wed 12:15
OPEN
May 2019
29
Wed 12:15
Xiaoming Mao, University of Michigan
e-mail: