Workshop 3: Modeling and Computation of Transmembrane Transport

(November 16,2015 - November 20,2015 )

Organizers


Benoit Roux
Pediatrics, Biochemistry & Molecular Biology, University of Chicago
Guowei Wei
Department of Mathematics, Michigan State University
Marie-Therese Wolfram

All fundamental self-sustaining processes of living organisms are based on their ability to receive, process, create and transmit signals. Human sensory systems receive a vast variety of signals, including photonic, acoustic, thermal, mechanical, and chemical ones. All of these signals must be converted into electric signals for the brain to process. Ion channels are the devices that transform all kind of mechanical, physical, and chemical signals into electric signals, which are transferred to the brain via neurons. Ion channels control a wide variety of important physiological processes, ranging from nerve and muscle excitation, muscle contraction, action potential generation and resting, sensory transduction, cell volume and blood pressure regulation, cell proliferation, hormone secretion, fertilization, maintenance of salt and water balance, metabolism of certain viruses, neurotoxicology, learning and memory, to programmed cell death. Some genetic diseases (channelopathies) are directly linked to malfunctioning of ion channel components. The impact of trauma or chronic traumatic encephalopathy on cell membranes, ion channels of axons and neurons and astrocytes is an active research front. Ion channel aggregation and collective motion play a significant role in synaptic plasticity and memory. Due to their paramount importance, there is a huge ion-channel community in contemporary biology. About 40% of all drugs target ion channels. Similarly, gap junctions are intercellular channels that allow various molecules and ions to pass between cells. Transmembrane brushes and transmembrane transporters are important for maintaining a proper material balance in cells. Ion channels, gap junctions and transmembrane transporters can vary two orders in their spatial and time scales. Currently, the study of ion channels, gap junctions and transmembrane transporters is an underrepresented field in the mathematical biology community. Apparently, a major barrier for mathematical scientists to work in this exciting field is the lack of knowledge concerning recent experiments on ion channels and gap junctions, while a major barrier for biologists in formulating sophisticated computational models is their lack of knowledge concerning the development in the last couple decades of modern mathematical tools and techniques. This workshop is designed to help bridge gaps between biologists and mathematicians. This workshop will cover a wide range of topics in mathematical modeling of ion channels and gap junctions, and their applications to specific research problems. The specific range will of course depend on the ultimate list of participants and speakers, but example topics are ion channels structures; ion channel-membrane interaction; ion channel gating mechanism; ion channel-neuron interfaces; Brownian dynamics; Langevin dynamics; stochastic models; rare event analysis; Markov process and master equation; molecular dynamics; mean field models; generalized Poisson-Nernst-Planck equations; electro-elastic models; fluid-electro-elastic models; complex fluid; inverse design; micro-macro models; continuum-discrete models; electrohydrodynamics of ion channel systems; and differential geometry based multiscale models. Emphasis will be placed on the application of the aforementioned models, theories, methods and algorithms to the better understanding of the structure, dynamics and transport of ion channels and gap junctions. This workshop will take the advantage of recently mathematical advances in stochastic and stochastic-hybrid systems for ion channel analysis. This workshop will significantly strengthen the existing collaborations between mathematicians and biologists, broaden their horizons to higher synergies, and further stimulate information flow "from biology to mathematics", i.e., to introduce new bio-inspired mathematical models, such as partial differential equations (PDEs), molecular manifolds, molecular Euler characteristics, etc, to graduate students and recent doctoral recipients.

Accepted Speakers

Simon Bernèche
Claudio Berti
Molecular Biophysics and Physiology, Rush University Medical Center
Michael Booty
Mathematical Sciences, None
Duan Chen
Department of Mathematics, University of North Carolina, Charlotte
Berend de Groot
Ke Dong
Robert Eisenberg
Molecular Biophysics and Physiology, Rush University Medical Center
Shelagh Ferguson-Miller
Dirk Gillespie
Molecular Biophysics and Physiology, Rush University Medical Center
Ulrich Kleinekathöfer
Maria Kurnikova
Tai-Chia Lin
Chun Liu
Mathematics, Penn State University
Benzhuo Lu
Inst. of Computational Mathematics, Chinese Academy of Sciences
Heather Mayes
Crina Nimigean
Perumal Nithiarasu
College of Engineering, Swansea University
Jan-Frederik Pietschmann
Keith Promislow
Mathematics, Michigan State University
Walter Rocchia
Riccardo Sacco
Ulrich Zachariae
Huan-Xiang Zhou
Yongcheng Zhou
Mathematics, Colorado State University
Monday, November 16, 2015
Time Session
07:45 AM

Shuttle to MBI

08:00 AM
08:30 AM

Breakfast

08:30 AM
08:45 AM

Welcome, overview, introduction: Marty Golubisky

08:45 AM
09:00 AM

Introduction by workshop organizers

09:00 AM
09:45 AM
Shelagh Ferguson-Miller - The Translocator Protein 18kDa

Abstract not submitted.

09:45 AM
10:30 AM
Simon Bernèche - Regulation of conductance in K channels

Abstract not submitted.

10:30 AM
11:00 AM

Break

11:00 AM
11:45 AM
Heather Mayes - Proton driven membrane transport by proteins

Abstract not submitted.

11:45 AM
12:30 PM
Claudio Berti - Brownian Dynamics simulations of ion channels

Abstract not submitted.

12:30 PM
02:00 PM

Lunch Break

02:00 PM
02:45 PM
Ulrich Kleinekathöfer - MD modeling of ion and antibiotics transport through porins

Abstract not submitted.

02:45 PM
03:00 PM

Break

03:00 PM
04:00 PM
Benoit Roux - Colloquium: Progress in understanding C-type inactivation

Abstract not submitted.

04:00 PM
06:00 PM

Reception and poster session in MBI Lounge

06:00 PM

Shuttle pick-up from MBI

Tuesday, November 17, 2015
Time Session
08:00 AM

Shuttle to MBI

08:15 AM
09:00 AM

Breakfast

09:00 AM
09:45 AM
Ke Dong - Voltage-gated sodium channels

Abstract not submitted.

09:45 AM
10:30 AM
Guowei Wei - Multiscale modeling of voltage-gated sodium channels

Abstract not submitted.

10:30 AM
11:00 AM

Break

11:00 AM
11:45 AM
Huan-Xiang Zhou - Membrane proteins: from structure refinement and remodeling to functional mechanisms

Abstract not submitted.

11:45 AM
12:30 PM
Crina Nimigean - Ion channel gating

Abstract not submitted.

12:30 PM
02:00 PM

Lunch Break

02:00 PM
02:45 PM
Berend de Groot - The molecular dynamics of permeation across biological membranes

Abstract not submitted.

02:45 PM
03:00 PM

Break

03:00 PM
03:45 PM
Ulrich Zachariae - Molecular Mechanisms of Selective and Efficient Ion Translocation Across Biological Membranes

Abstract not submitted.

03:45 PM
04:30 PM

Informal discussions/daily wrap-up

04:30 PM

Shuttle pick-up from MBI

Wednesday, November 18, 2015
Time Session
08:00 AM

Shuttle to MBI

08:15 AM
09:00 AM

Breakfast

09:00 AM
09:45 AM
Perumal Nithiarasu - Calcium dynamics and vasomotion

Abstract not submitted.

09:45 AM
10:30 AM
Yongcheng Zhou - Dual phase field modeling of endocytosis

Abstract not submitted.

10:30 AM
11:00 AM

Break

11:00 AM
11:45 AM
Michael Booty
11:45 AM
12:30 PM
Benzhuo Lu - A platform for finite element modeling of ion transport in ion channels and nanopores

Abstract not submitted.

12:30 PM
02:00 PM

Lunch Break

02:00 PM
02:45 PM
Marie-Therese Wolfram - Inverse problems for biological and synthetic pores

Abstract not submitted.

02:45 PM
03:00 PM

Break

03:00 PM
03:45 PM
Keith Promislow - Models of ionic channels

Abstract not submitted.

03:45 PM
04:30 PM

Informal discussions/daily wrap-up

04:30 PM

Shuttle pick-up from MBI

Thursday, November 19, 2015
Time Session
08:00 AM

Shuttle to MBI

08:15 AM
09:00 AM

Breakfast

09:00 AM
09:45 AM
Robert Eisenberg - Reduced Models of Ion Permeation

Abstract not submitted.

09:45 AM
10:30 AM
Chun Liu - Transport of charged particles through biological environments

Abstract not submitted.

10:30 AM
11:00 AM

Break

11:00 AM
11:45 AM
Tai-Chia Lin - Poisson-Nernst-Planck equations

Abstract not submitted.

11:45 AM
12:30 PM
Dirk Gillespie - TBA

Abstract not submitted.

12:30 PM
02:00 PM

Lunch Break

02:00 PM
02:45 PM
Maria Kurnikova - Modeling and Simultion Approaches for Ion Permeation and Gating in Protein Ion Channels

Abstract not submitted.

02:45 PM
03:00 PM

Break

03:00 PM
03:45 PM
Walter Rocchia - Accepted Recent advances on continuum models describing nanoscale electric phenomena

Abstract not submitted.

03:45 PM
04:30 PM

Informal discussions/daily wrap-up

04:30 PM

Shuttle pick-up from MBI

06:30 PM
07:00 PM

Cash bar

07:00 PM
07:00 PM

Banquet in the Fusion Room @ Crowne Plaza Hotel

Friday, November 20, 2015
Time Session
08:00 AM

Shuttle to MBI

08:15 AM
09:00 AM

Breakfast

09:00 AM
09:45 AM
Jan-Frederik Pietschmann - Nonlinear models for nanopores

Abstract not submitted.

09:45 AM
10:30 AM
Duan Chen - Modeling and computation of heterogeneous implicit solvent and its applications for biomolecules

Abstract not submitted.

10:30 AM
11:00 AM

Break

11:00 AM
11:45 AM
Riccardo Sacco - Electrodiffusion of ions through protein membrane channels

Abstract not submitted.

11:45 AM
12:00 PM

Informal discussions/workshop wrap-up

12:00 PM

Shuttle pick-up from MBI

Name Email Affiliation
Bernèche, Simon simon.berneche@unibas.ch
Berti, Claudio Claudio_Berti@rush.edu Molecular Biophysics and Physiology, Rush University Medical Center
Booty, Michael booty@njit.edu Mathematical Sciences, None
Cang, Zixuan cangzx@gmail.com Department of mathematics, Michigan State University
Capponi, Sara scapponi@uci.edu
Chen, Duan dchen10@uncc.edu Department of Mathematics, University of North Carolina, Charlotte
de Groot, Bert bgroot@gwdg.de
Dong, Ke dongk@msu.edu
Eisenberg, Robert beisenbe@rush.edu Molecular Biophysics and Physiology, Rush University Medical Center
Ferguson-Miller, Shelagh fergus20@msu.edu
Gillespie, Dirk Dirk_Gillespie@rush.edu Molecular Biophysics and Physiology, Rush University Medical Center
Herschlag, Gregory gjh@math.duke.edu Mathematics, Duke University
Im, Wonpil wonpil@ku.edu Molecular Biosciences and Center for Computational Biology, The University of Kansas
Kleinekathoefer, Ulrich u.kleinekathoefer@jacobs-university.de
Kurnikova, Maria kurnikova@cmu.edu
Li, Jingyuan lijingyuan@ihep.ac.cn
Lin, Tai-Chia tclin@math.ntu.edu.tw
Liu, Chun liu@math.psu.edu Mathematics, Penn State University
Lu, Benzhuo bzlu@lsec.cc.ac.cn Inst. of Computational Mathematics, Chinese Academy of Sciences
Matejczyk, Bartlomiej bartlomiej.matejczyk@ricam.oeaw.ac.at Radon Institute computational and applied mathematics, RICAM
Mayes, Heather hmayes@cmayes.com
Mu, Lin linmu@math.msu.edu Department of Mathematics, Michigan State University
Ngo, Van snoskov@ucalgary.ca
Nimigean, Crina crn2002@med.cornell.edu
Nithiarasu, Perumal P.Nithiarasu@swansea.ac.uk College of Engineering, Swansea University
Opron, Kristopher opronkri@msu.edu Biochemistry, Michigan State University
Pietschmann, Jan-Frederik pietschmann@mathematik.tu-darmstadt.de
Pomes, Regis pomes@sickkids.ca
Promislow, Keith kpromisl@math.msu.edu Mathematics, Michigan State University
Rocchia, Walter walter.rocchia@iit.it
Roux, Benoit roux@uchicago.edu Pediatrics, Biochemistry & Molecular Biology, University of Chicago
Sacco, Riccardo riccardo.sacco@polimi.it
Wei, Guowei wei@math.msu.edu Department of Mathematics, Michigan State University
Wu, Kedi vettelwu@gmail.com Mathematics, Michigan State University
Xia, Kelin xiakelin@msu.edu MATHEMATICS, Michigan State University
Yan, Jue jyan@iastate.edu Mathematics, Iowa State University
Yang, Lijian lijian_yang@phy.ccnu.edu.cn
Young, Yuan-Nan yyoung@njit.edu Department of Mathematical Sciences, New Jersey Institute of Technology
Zachariae, Ulrich u.zachariae@dundee.ac.uk
Zanella, Mattia mattia.zanella@unife.it
Zhou, Huan-Xiang hzhou4@fsu.edu
Zhou, Yongcheng yzhou@math.colostate.edu Mathematics, Colorado State University
Regulation of conductance in K channels

Abstract not submitted.

Brownian Dynamics simulations of ion channels

Abstract not submitted.

Modeling and computation of heterogeneous implicit solvent and its applications for biomolecules

Abstract not submitted.

The molecular dynamics of permeation across biological membranes

Abstract not submitted.

Voltage-gated sodium channels

Abstract not submitted.

Reduced Models of Ion Permeation

Abstract not submitted.

The Translocator Protein 18kDa

Abstract not submitted.

TBA

Abstract not submitted.

MD modeling of ion and antibiotics transport through porins

Abstract not submitted.

Modeling and Simultion Approaches for Ion Permeation and Gating in Protein Ion Channels

Abstract not submitted.

Poisson-Nernst-Planck equations

Abstract not submitted.

Transport of charged particles through biological environments

Abstract not submitted.

A platform for finite element modeling of ion transport in ion channels and nanopores

Abstract not submitted.

Proton driven membrane transport by proteins

Abstract not submitted.

Ion channel gating

Abstract not submitted.

Calcium dynamics and vasomotion

Abstract not submitted.

Nonlinear models for nanopores

Abstract not submitted.

Models of ionic channels

Abstract not submitted.

Accepted Recent advances on continuum models describing nanoscale electric phenomena

Abstract not submitted.

Colloquium: Progress in understanding C-type inactivation

Abstract not submitted.

Electrodiffusion of ions through protein membrane channels

Abstract not submitted.

Multiscale modeling of voltage-gated sodium channels

Abstract not submitted.

Inverse problems for biological and synthetic pores

Abstract not submitted.

Molecular Mechanisms of Selective and Efficient Ion Translocation Across Biological Membranes

Abstract not submitted.

Membrane proteins: from structure refinement and remodeling to functional mechanisms

Abstract not submitted.

Dual phase field modeling of endocytosis

Abstract not submitted.