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Subject: SMB Digest v13i33
SMB Digest August 13, 2013 Volume 13 Issue 33
ISSN 1086-6566
Editor: Richard Schugart richard(dot)schugart(at)gmail(dot)com
Note:
Information about the Society for Mathematical Biology, including an
application for membership, may be found in the SMB Home Page,
http://www.smb.org/ .
Access the Bulletin of Mathematical Biology, the official journal of
SMB, at http://www.springer.com/11538 .
Inquiries about membership or BMB fulfillment should be sent to
membership(at)smb(dot)org .
Issue's Topics:
SMB September 2013 Newsletter Submission Request
CfN: Julian Cole Lectureship 2014, SIAM
Newsletter: NIMBioS, U Tennessee, Knoxville
ToC: BMB, Volume 75, Issue 8
ToC: Molecular Based Mathematical Biology, Vol 1, Issue 1
PhD Position: Plant Cell Biomechanics, U Dundee
PhD Position: Yeast Stress Response, Imperial College
Post-doc: Stochastic Biochemical Kinetics, U Edinburgh
Post-doc: Computational Systems Biology, U Coimbra, Portugal
Post-doc: Grabe Lab, U Pittsburgh
Tenure-Track: Mathematical Biology, U Idaho, US
Tenure-Tracks: Applied Mathematics, U Colorado-Boulder
SMBnet Reminders
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From: ELADDADI, AMINA <eladdada@mail.strose.edu>
Date: August 7, 2013 2:12:46 PM
Subject: SMB September 2013 Newsletter Submission Request
Been to an interesting conference in the last few months? Planning an
interesting conference? Do you have an opinion about mathematical
biology? Is there a hot new area we should know about? Contribute to
the next issue of the SMB Newsletter to appear in September 2013, by
sending materials to: Editor(at)smb(dot)org.
We invite submissions including summaries of previous mathematical
biology meetings, invitations to upcoming conferences, commentaries,
book reviews or suggestions for other future columns. The deadline is
the 15th of the month prior to publication.
The SMB Newsletter is published in January, May and September by the
Society for Mathematical Biology for its members.
Check out the previous SMB newsletters:
http://www.smb.org/publications/newsletter.shtml
----------------------------------------------------
From: J. M. Littleton <Littleton@siam.org>
Date: August 10, 2013 12:36:57 AM
Resent-From: Raymond Mejía <mejiar@helix.nih.gov>
Subject: CfN: Julian Cole Lectureship 2014, SIAM
CALL FOR NOMINATIONS
Julian Cole Lecture
The Julian Cole Lecture is awarded every four years to a member of the
scientific or engineering community for an outstanding contribution to
the mathematical characterization and solution of a challenging problem
in the physical or biological sciences, or in engineering, or for a
development of mathematical methods for the solution of such problems.
The prize will be awarded and the Cole Lecture delivered at the 2014
SIAM Annual Meeting (AN14), to be held July 7-11, 2014, in Chicago,
Illinois.
Description of the Award
The award consists of a certificate and a cash prize of $1,000. The
recipient will deliver the Julian Cole Lecture at the annual meeting.
SIAM will reimburse the Cole Lecturer's travel expenses to attend the
meeting to receive the award and deliver the lecture.
Nominations
Nominations should be sent to cole_lecture@siam.org by OCTOBER 15, 2013.
Attach a letter of nomination, including a description of the
contribution, a CV of the candidate, and letters of support from two or
three experts (not more than three letters). Letters should be
addressed as below:
Chair
Julian Cole Lecture Committee
c/o J. M. Littleton
SIAM
3600 Market Street, 6th Floor
Philadelphia, PA 19104-2688
E-mail: littleton@siam.org
Phone: +1-215-382-9800 ext. 303
Selection Committee
The members of the committee are: M. Gregory Forest (Chair), University
of North Carolina; Suzanne Lenhart, University of Tennessee Knoxville;
Michael Shelley, Courant Institute-NYU.
----------------------------------------------------
From: NIMBioS <newsletter@nimbios.org>
Date: August 7, 2013 12:10:44 PM
Subject: Newsletter: NIMBioS, U Tennessee, Knoxville
For the bi-monthly newsletter of the National Institute for Mathematical
and Biological Synthesis (NIMBioS), go to
http://archive.constantcontact.com/fs105/1102610363105/archive/1114430117218.html
----------------------------------------------------
From: Springer <springeralerts@springer.delivery.net>
Date: August 13, 2013 2:02:27 AM
Subject: ToC: BMB, Volume 75, Issue 8
Volume 75 Number 8 is now available on SpringerLink
http://link.springer.com/journal/11538/75/8/page/1
IN THIS ISSUE:
Biomedical Modeling: The Role of Transport and Mechanics
Mark Alber, Philip K. Maini & Glen Niebur
Tendon Mechanobiology: Experimental Models Require Mathematical
Underpinning
Mark S. Thompson
The Influence of Hindered Transport on the Development of Platelet
Thrombi Under Flow
Karin Leiderman & Aaron L. Fogelson
Experimental and Computational Investigation of the Role of Stress Fiber
Contractility in the Resistance of Osteoblasts to Compression
P. P. Weafer, W. Ronan, S. P. Jarvis & J. P. McGarry
A Hybrid Model of Tumor?Stromal Interactions in Breast Cancer
Yangjin Kim & Hans G. Othmer
Negative Tension of Scroll Wave Filaments and Turbulence in
Three-Dimensional Excitable Media and Application in Cardiac Dynamics
Sergio Alonso, Markus Bär & Alexander V. Panfilov
A Cell-Based Model of Extracellular-Matrix-Guided Endothelial Cell
Migration During Angiogenesis
Josephine T. Daub & Roeland M. H. Merks
Modeling Intercellular Transfer of Biomolecules Through Tunneling
Nanotubes
Yasir Suhail, Kshitiz, Justin Lee, Mark Walker, Deok-Ho Kim,
Matthew D. Brennan, Joel S. Bader & Andre Levchenko
----------------------------------------------------
From: Shan Zhao <szhao@bama.ua.edu>
Date: August 9, 2013 2:05:27 AM
Subject: ToC: Molecular Based Mathematical Biology, Vol 1, Issue 1
Table of Contents
Molecular Based Mathematical Biology (MBMB)
Volume 1, Number 1.
Editors of the Inaugural Issue: Shan Zhao, Julie Mitchell, Yongcheng
Zhou, and Weihua Geng.
Langhua Hu, Duan Chen, and Guowei Wei, High-order fractional partial
differential equation transform for molecular surface construction,
1-25.
M.R. Swager and Y.C. Zhou, Genetic Exponentially Fitted Method for
Solving Multi-dimensional Drift-diffusion Equations, 26-41.
Chuan Li, Lin Li, Marharyta Petukh, and Emil Alexov, Progress in
developing Poisson-Boltzmann equation solvers, 42-62.
Robert C. Harris, Travis Mackoy, and Marcia O. Fenley, A Stochastic
Solver of the Generalized Born Model, 63-74.
Atilla Sit, Julie C Mitchell, George N Phillips, and Stephen J Wright,
An Extension of 3D Zernike Moments for Shape Description and Retrieval
of Maps Defined in Rectangular Solids, 75-89.
Yan Xie, Jie Cheng, Benzhuo Lu, and Linbo Zhang, Parallel Adaptive
Finite Element Algorithms for Solving the Coupled Electro-diffusion
Equations, 90-108.
Weihua Geng and Shan Zhao, Fully implicit ADI schemes for solving the
nonlinear Poisson-Boltzmann equation, 109-123.
Amelia B. Kreienkamp, Lucy Y. Liu, Mona S. Minkara, Matthew G. Knepley,
Jaydeep P. Bardhan, and Mala L. Radhakrishnan, Analysis of fast
boundary-integral approximations for modeling electrostatic
contributions of molecular binding, 124-150.
Nikolay A. Simakov and Maria G. Kurnikova, Graphical Processing Unit
accelerated Poisson equation solver and its application for calculation
of single ion potential in ion-channels, 151-163.
Tao Liao, Yongjie Zhang, Peter M. Kekenes-Huskey, Yuhui Cheng, Anushka
Michailova, Andrew D. McCulloch, Michael Holst, and J. Andrew McCammon,
Multi-core CPU or GPU-accelerated Multiscale Modeling for Biomolecular
Complexes, 164-179.
Instructions for Authors and Online Open Access:
http://www.degruyter.com/view/j/mlbmb
----------------------------------------------------
From: Mariya Ptashnyk <mptashnyk@maths.dundee.ac.uk>
Date: August 9, 2013 11:20:47 AM
Subject: PhD Position: Plant Cell Biomechanics, U Dundee
PhD studentship in Applied Mathematics/Mathematical Biology
Plant cell biomechanics: Mathematical modelling and analysis of the
interactions between plant cell microtubules and cell wall microfibrils
Cell expansion in plants is fundamental for morphogenesis and growth.
The main force for cell elongation (the internal turgor pressure) acts
isotropically, and so it is the microscopic structure of the cell wall,
surrounding each plant cell, that controls the anisotropic growth of
plant cells and tissue. A key regulatory element of anisotropic growth
is the directional deposition of cellulose microfibrils (MF). The
orientation of MF, their length, high tensile strength and interaction
with wall matrix macro-membrane molecules (e.g. pectin, hemicellulose)
strongly influences the pectin wall stiffness. MF are synthesized by
plasma membrane-located cellulose synthase complexes that move along
cortical microtubules. Thus it is assumed that cortical microtubules
influence the deposition direction of MF and impact the mechanical
properties of plant cell walls.
Cortical microtubules (CMT) are highly dynamic structures, nucleated at
the plant cell cortex and attached to the plasma membrane by linker
proteins. CMT are arranged and organised in different patterns, relying
on a variety of mechanisms for assembly, orientation and function.
Along with the alignment hypothesis, new experiments have shown possible
ordered deposition or stochastic distribution of MF in the absence of
assembled CMT (distorted by microtubule-depolymerizing drugs), whereas
the inhibition of MF synthesis prevents the characteristic orientation
of CMT. Thus an important biological question and mathematical challenge
is to model and to understand the correlation between CMT and MF
alignment and reorientation.
The main focus of the research project will be on the mathematical
modelling of CMT dynamics and interactions between CMT and MF, as well
as analysis and numerical simulations of the developed models. A
continuous approach using systems of partial and ordinary differential
equations will be considered to derive new mathematical models for CMT.
The theoretical research will be conducted in collaboration with
experimental biologists at the James Hutton Institute, Dundee, UK and
University of Heidelberg, Germany. The analysis of model equations and
comparison of numerical solutions with experimental data will help to
understand the main mechanisms underlying CMT-MF interactions and their
reorientations in response to external and internal forces.
The successful candidate will have a background in mathematics and an
interest in the interface between mathematics and biology. Together with
a Post-Doctoral fellow and experimental partners the successful
candidate will form a team investigating the fascinating microscopic
mechanical properties of plant cells. Because of EPSRC restrictions, the
full studentships will be available only to UK residents. (For complete
information on students eligibility, please consult the EPSRC website
http://www.epsrc.ac.uk/skills/students/help/Pages/eligibility.aspx).
The studentship is for 42 months.
If you are interested in this PhD position please contact Mariya
Ptashnyk, Division of Mathematics, University of Dundee,
mptashnyk@maths.dundee.ac.uk. Please include a cover letter, a full CV
detailing the taken undergraduate courses and corresponding grades, as
well as contact information of two referees.
----------------------------------------------------
From: Shahrezaei, Vahid <v.shahrezaei@imperial.ac.uk>
Date: August 12, 2013 5:49:25 AM
Subject: PhD Position: Yeast Stress Response, Imperial College
We have a PhD position available at Imperial College to study stress
response in yeast using an integrated experimental and computational
approach.
Candidates with either biological or mathematical backgrounds would be
considered. The deadline for application is 31st of August. For more
details please see:
http://www.findaphd.com/search/ProjectDetails.aspx?PJID=46385
----------------------------------------------------
From: Ramon Grima <ramon.grima@ed.ac.uk>
Date: August 6, 2013 9:11:53 AM
Subject: Post-doc: Stochastic Biochemical Kinetics, U Edinburgh
POSTDOCTORAL POSITION IN STOCHASTIC BIOCHEMICAL KINETICS
Applications are invited for a postdoctoral research assistant to work
on an interdisciplinary project aiming to develop a stochastic theory of
chemical kinetics in non-dilute & macromolecular crowded environments
i.e. the typical conditions characterizing the intracellular
environment. The start date for the project is 1st November 2013 or as
soon as possible after this date.
This is for a theoretical physicist, theoretical chemist or applied
mathematician with a solid background in non-equilibrium statistical
physics (Master equations / Fokker-Planck equations). Programming skills
in C or Fortran and experience in Matlab/Mathematica are highly
desirable.
The position is in the group of Dr. Ramon Grima
http://grimagroup.bio.ed.ac.uk/index.html at the University of Edinburgh
and is for 30 months. The successful candidate is expected to regularly
interact with an experimental postdoctoral researcher in the lab of
Prof. Manfred Auer who will be testing the new stochastic theories
developed within this project. The candidate will additionally benefit
from the excellent interdisciplinary atmosphere of the Center for
Synthetic and Systems Biology (SynthSys) which is housed in a
purpose-built facility on the Kings Building campus of the University of
Edinburgh.
The job is vacancy 017762 on the University of Edinburgh's job vacancy
website through which applications are accepted.
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.
----------------------------------------------------
From: Armindo Salvador <armindo.salvador@gmail.com>
Date: August 8, 2013 10:54:08 AM
Subject: Post-doc: Computational Systems Biology, U Coimbra, Portugal
The Molecular Systems Biology Group at the Center for Neuroscience and
Cell Biology (CNCB) ? University of Coimbra, is seeking highly motivated
candidates for a post?doctoral fellowship under the project
FCOMP?01?0124?FEDER?020978 (FCT ref.: PTDC/QUI?BIQ/119657/2010)
"Finding the naturally evolved design principles of prevalent metabolic
circuits". Applicants of any nationality must have a Ph. D. degree by
the application deadline, a documented strong mathematical and
computational background, and a strong publication record in
bioinformatics, computational systems biology or related areas.
Documented experience in mathematical modeling of biochemical processes
is a strong preferential condition.
The object of activity will be the characterization of principles of
quantitative design of metabolic network motifs through mathematical
modeling, systems analysis and analysis of experimental data. The
fellowship will have the duration of 12 months and start October 2013
(negotiable date). Eventual renewal will be based on merit and
availability of funds. The monthly salary (tax free) will be 1495 euros.
Applications can be submitted by email to armindo.salvador@gmail.com,
from August 1 to September 5, 2013. They must indicate reference
BPD2/PTDC/QUI?BIQ/119657/2010 and include all the following documents:
motivation letter, curriculum vitae, publications list, copy of Ph. D.
diploma/certificate, and contact information (email and phone) of at
least three references.
For further information please see
http://www.eracareers.pt/opportunities/index.aspx?task=global&jobId=38329
----------------------------------------------------
From: Grabe, Michael David <mdgrabe@pitt.edu>
Date: August 8, 2013 7:00:56 PM
Subject: Post-doc: Grabe Lab, U Pittsburgh
A postdoctoral position is currently available in the Grabe lab at the
University of Pittsburgh, Department of Biological Sciences to develop
mechanical models of membranes. This work is currently supported by an
NSF CAREER award, and it is aimed at using continuum elasticity theory
to describe membrane deformations around embedded membrane proteins.
Qualified candidates will have a strong applied mathematics background
with detailed experience in elasticity theory, finite difference and/or
finite element methods, level set methods, and a deep interest in
biological phenomena. Candidates that also have a background in
computational and structural biology are encouraged to apply. Models
will be applied to understanding phenomena at the nanometer scale such
as protein assisted membrane fusion, membrane protein stability, and
permeation of small molecules and peptides across membranes. Studies
will be carried out in close collaboration with experimental labs.
The salary range will follow the NIH standard and will depend on the
applicants experience. The position comes with health insurance and full
benefits provided through the University of Pittsburgh. For more
information on the Grabe Lab please visit our website
http://mgrabe1.bio.pitt.edu/
Interested individuals should send their applications to Michael Grabe:
mdgrabe@pitt.edu
----------------------------------------------------
From: Christina Towler <christina@jobelephant.com>
Date: August 8, 2013 5:39:10 PM
Subject: Tenure-Track: Mathematical Biology, U Idaho, US
The Department of Mathematics at the University of Idaho invites
applications for a tenure-track faculty position in Mathematical
Biology. This is part of a three-position cluster hire to be filled
(with the other two in Statistics and Physics) that will address aspects
of Systems Biology. This is an academic year (9-month) position at the
rank of Assistant Professor beginning August 17, 2014. Responsibilities
include: carrying out an active research program and teaching courses at
the undergraduate and graduate levels. Women and minorities are
especially encouraged to apply. AA/EOE
Opportunities for interdisciplinary interactions abound. The Department
of Biological Sciences has strengths in evolutionary biology, microbial
ecology, reproductive biology, cellular and molecular biology and
biochemistry. The Institute for Bioinformatics and Evolutionary Studies
(IBEST) includes researchers from many departments (Biology, Computer
Science, Mathematics, Statistics, Physics, and Chemistry) and focuses on
research in evolution through a variety of approaches (experimental
evolution of microorganisms, mathematical/computational modeling,
genomics, and field biology).
CLOSING DATE: Review of applications will begin November 1, 2013, and
continue until a suitable applicant pool is identified. Please direct
any questions regarding this position to math@uidaho.edu.
For a complete description of the announcement, how to apply, and
information about the department, visit http://apptrkr.com/378796.
----------------------------------------------------
From: DM Bortz <Dmbortz@Colorado.EDU>
Date: August 7, 2013 8:25:26 PM
Subject: Tenure-Tracks: Applied Mathematics, U Colorado-Boulder
The Department of Applied Mathematics at the University of Colorado
Boulder seeks to hire two tenure-track Assistant Professors to begin
August 2014. The first position is in the area of nonlinear mathematics
and applications and the second position is in the area of
computational/numerical mathematics and applications; however,
exceptional candidates in all fields of Applied Mathematics may be
considered. The candidate is expected to take an active role in
undergraduate and graduate teaching, conduct an active, externally
funded research program, and advise graduate students. A Ph.D. in
Applied Mathematics, Mathematics, or related discipline is required.
Authority to fill this position is pending budgetary approval. Review of
applications will begin October 1, 2013 and continue until finalists are
identified.
The Applied Mathematics Department has significant research efforts in
computational mathematics, mathematical biology, physical applied
mathematics, probability, statistics, and nonlinear mathematics
including nonlinear dynamics and waves. For more information, see
http://amath.colorado.edu/. The University of Colorado Boulder offers a
rich research environment, with numerous interdisciplinary initiatives
in the physical and life sciences.
The University of Colorado is an Equal Opportunity Employer committed to
building a diverse workforce. We encourage applications from women,
racial and ethnic minorities, individuals with disabilities, and
veterans. Alternative formats of this posting can be provided upon
request for individuals with disabilities by contacting the ADA
Coordinator at hr-ada@colorado.edu. See
www.colorado.edu/ArtsSciences/Jobs/ for additional information.
Applications are accepted electronically at https://www.jobsatcu.com,
postings #F00596 and #F00595.
----------------------------------------------------
Subject: SMBnet Reminders
To subscribe to the SMB Digest please point your browser at
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After you subscribe, you will receive a greeting with additional
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Submissions to appear in the SMB Digest may be sent to
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Items of interest to the mathematical biology community may be submitted
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The SMB Digest is also available on the SMB Home Page at
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The contents of this publication may be reproduced in whole or in part
with attribution.
End of SMB Digest
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