Subject: Society for Mathematical Biology Digest

SMB Digest  January 20, Volume 16  Issue 3
ISSN 1086-6566

Editor: Wandi Ding: ding.smb.digest(at)gmail(dot)com

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:
   NIH T90/R90: Training in Computational Neuroscience
   Council Meeting, New Investigator Funding Rates, ...
   Contents, Molecular Based Mathematical Biology, Vol. 3
   Deadline extension: Workshop on Teaching Computational Science...
   AMNS-2016 Conference and ..., Kathmandu, Nepal, May 26-29
   STEP Program: Molecular & Integrative Physiology, May 31-Aug. 19
   Summer School: Mathematical Modeling..., Ohio, June 13-22
   Workshop: Quantitative Laws..., Como, Italy, June 13-25
   Workshop: Algebraic Mathematical Biology, NIMBioS, July 25-27 
   Summer school: Structured populations, Finland, August 21-28 
   Workshop: Quantitative Biomedicine for Health and Disease
   PhD Studentship: Mathematical Ecology, Univ of Dundee, UK 
   PhD studentship, Dynamical Systems..., Univ of Auckland
   Lectureship, Mathematical Biology/Medicine, Univ of Exeter
   SMBnet Reminders


From: Whang, Kenneth C. <kwhang@nsf.gov>
Date: Thu, Jan 14, 2016 at 10:36 AM
Subject: NIH T90/R90: Training in Computational Neuroscience

The NIH Blueprint for Neuroscience Research has reissued the Funding 
Opportunity Announcement (FOA) for "Training in Computational Neuroscience: 
From Biology to Model and Back Again (T90/R90)" 
(see http://grants.nih.gov/grants/guide/rfa-files/RFA-DA-16-009.html).
This FOA will support integrated research education and research training 
programs that provide interdisciplinary training in experimental 
neuroscience and the theoretical and technological approaches of 
computational neuroscience at the undergraduate and predoctoral level. 
New applications and renewal applications from current grantees are both 
Each application:
Must include a full-time undergraduate research training component that will 
combine coursework and hands-on laboratory research experience (R90);
Must include a full-time Ruth L. Kirschstein National Research Service Award 
(NRSA) institutional predoctoral training component (T90); May include a 
full-time non-NRSA institutional predoctoral training component (R90); May 
include a short-term research education component (e.g., short course or 
workshop) that may include scientists at any stage of the career continuum 
as participants (R90).[Optional]
For further information, contact:
Susan Volman, PhD
Program Director
Ph: 301-435-1315
E-mail: svolman@nida.nih.gov


From: Dieffenbach, Ann (NIH/NIGMS) [E] <DIEFFENA@NIGMS.NIH.GOV>
Date: Thu, Jan 14, 2016 at 2:52 PM
Subject: Council Meeting, New Investigator Funding Rates, ...


--Advisory Council Meeting
--New Investigator Funding Rates Analysis
--FY 2016 Financial Management Plan
--Funding Opportunities

See https://list.nih.gov/cgi-bin/wa.exe?A2=nigms_network;1d718b69.1601


From: Zhao, Shan <szhao@ua.edu>
Date: Thu, Jan 14, 2016 at 8:00 AM
Subject: Contents, Molecular Based Mathematical Biology, Vol. 3

Table of Contents, Molecular Based Mathematical Biology, Vol. 3, 2015
Open access, full text available at http://www.degruyter.com/view/j/mlbmb

1. Nonlocal Electrostatics in Spherical Geometries Using Eigenfunction 
Expansions of Boundary-Integral Operators, Bardhan, Jaydeep P. / Knepley, 
Matthew G. / Brune, Peter
2. Topological Complexity in Protein Structures, Flapan, Erica / Heller, 
3. Curvature Concentrations on the HIV-1 Capsid, Liu, Jiangguo / 
Sadre-Marandi, Farrah / Tavener, Simon / Chen, Chaoping
4. A boundary integral Poisson-Boltzmann solvers package for solvated 
bimolecular simulations, Geng, Weihua
5. A topological approach for protein classification, Cang, Zixuan / Mu, Lin 
/ Wu, Kedi / Opron, Kristopher / Xia, Kelin / Wei, Guo-Wei
6. Fast and Robust Orientation of Cryo-Electron Microscopy Images, 
Xu, Guoliang / Wang, Xia / Li, Ming / Jing, Zhucui
7. A Quantum Corrected Poisson-Nernst-Planck Model for Biological Ion 
Channels, Liu, Jinn-Liang
8. Modeling and Simulation of Thermo-Fluid-Electrochemical Ion Flow in 
Biological Channels, Sacco, Riccardo / Manganini, Fabio / Jerome, Joseph W.
9. Shape Correspondence Analysis for Biomolecules Based on Volumetric 
Eigenfunctions, Liao, Tao / Lee, Hao-Chih / Yang, Ge /Zhang, Yongjie Jessica
10. Membrane-Channel Protein System Mesh Construction for Finite Element 
Simulations, Liu, Tiantian / Bai, Shiyang / Tu, Bin / Chen, Minxin / 
Lu, Benzhuo
11. SDPBS Web Server for Calculation of Electrostatics of Ionic Solvated 
Biomolecules, Jiang, Yi / Xie, Yang / Ying, Jinyong / Xie, Dexuan /Yu, Zeyun
12. Role of Dispersion Attraction in Differential Geometry Based Nonpolar 
Solvation Models, Chen, Zhan


From: Shiflet, Angela B. <ShifletAB@wofford.edu>
Date: Sun, Jan 17, 2016 at 2:38 PM
Subject: Deadline extension: Workshop on Teaching Computational Science...

The International Conference on Computational Science (ICCS 2016) 
(http://www.iccs-meeting.org/iccs2016/) and the The Workshop on Teaching 
Computational Science (http://webs.wofford.edu/shifletab/iccs/), which 
will be held in San Diego, California, U.S.A., June 6 - 8, have extended 
the paper submission deadlines to January 31, 2016. There are submission 
options for full paper and oral presentation without a paper (abstract only).  
Please let us know if you have any questions.

Co-Chairs of "The Workshop on Teaching Computational Science":
Angela B. Shiflet, Ph. D. (shifletab@wofford.edu), Wofford College, USA
Alfredo Tirado-Ramos, Ph. D. (mailto:TiradoRamos@uthscsa.edu), U. of Texas 
Health Science Center, USA


From: DAVID F ANDERSON <anderson@math.wisc.edu
Date: Mon, Jan 18, 2016 at 9:18 AM
Subject: Workshop: ADVANCES IN NUMERICAL AND ANALYTIC..., UK, April 4-8



4 April, 2016 - 8 April, 2016 INI, Cambridge, England, United Kingdom

Abstract: This workshop focuses on numerical methods and mathematical 
analysis for non-spatial stochastic dynamical models that arise in 
molecular biology. New experimental techniques at a molecular level boosted 
the interest for such models in recent years, for example for gene 
regulatory networks, biochemical signaling and transduction cascades, 
molecular motors, and morphogenesis. The workshop brings together 
computational, mathematical, and experimental scientists, with attention 
falling on both current research and promising avenues for future research. 
It reports on the exciting synergistic interplay between advanced 
experimental, computational, and mathematical techniques that together 
provide a deeper understanding of the biological system.


John Albeck (UC Davis)
Rosalind Allen (Edinburgh)
Kevin Burrage (Oxford and Queensland University of Technology)
Yang Cao (Virginia Tech)
Simon Cotter (Manchester)
Eric Deeds (Kansas)
Andrew Duncan (Imperial College London)
Omer Dushek (Oxford)
James Faeder (Pittsburgh)
Ramon Grima (Edinburgh)
Ankit Gupta (ETH )
Xingye Kan (University of Minnesota)
Markos Katsoulakis (University of Massachusetts)
Mustafa Khammash (ETH )
Allon Klein (Harvard)
Thomas Kurtz (University of Wisconsin)
Carlos Lopez (Vanderbilt)
Carmen Molina-Paris (University of Leeds)
Jay Newby (UNC)
Christian Ray (Kansas)
Vahid Shahrezaei (Imperial College London)
Erkki Somersal (Case Western Reserve)
Vikram Sunkara (Free U. Berlin)
Raul Tempone (KAUST)
Pieter Rein ten Wolde (FOM Institute/Amsterdam)
Thomas Vejchodsky(Institute of Mathematics at the Czech Academy of Sciences)
Darren Wilkinson (Newcastle)

More details and the application form are available here:


Closing date for applications: 12 February 2016

This workshop is part of a 6-month programme on "Stochastic Dynamical 
Systems in Biology: Numerical Methods and Applications" which is taking 
place at the Isaac Newton Institute (Cambridge, England) from January till 
June 2016. The programme will feature three workshops in Cambridge, as well 
as a satellite meeting in Edinburgh. More details about the whole programme 
can be found here: http://www.newton.ac.uk/event/sdb


From: Vaidya, Naveen K. <vaidyan@umkc.edu>
Date: Wed, Jan 20, 2016 at 10:10 AM
Subject: AMNS-2016 Conference and ..., Kathmandu, Nepal, May 26-29

The Association of Nepalese Mathematicians in America (ANMA), Nepal 
Mathematical Society (NMS) and mathematics departments of Tribhuvan 
University and Kathmandu University are jointly organizing the International 
Conference on Application of Mathematics to Nonlinear Science (AMNS-2016) 
in Kathmandu, Nepal, from May 26-29, 2016. The main objective of the 
conference is to provide a common platform for researchers, educators, 
business leaders, academic administrators, and government officials, among 
others, to share research interests and disseminate their research findings. 
One of the central themes of this conference is "Mathematical Biology". In 
addition, at the AMNS-2016 conference, there will be a Mathematical 
Biology Workshop (MBW) in May 26, 2016.
Some travel supports (sponsored by the Society for Mathematical Biology) 
are available for students and junior faculty from Nepal and neighboring 
developing countries. To receive support, the conference participants also 
need to attend Mathematical Biology Workshop. Please visit the MBW website 
http://anmaweb.org/AMNS-2016/MBW.html or contact the workshop organizer 
Dr. Naveen K. Vaidya (vaidyan@umkc.edu) for details on travel support.
We are delighted to mention that Kathmandu, the city of conference venue, 
is an eminent historical city and a hub of world cultural heritage sites. 
Please visit the AMNS-2016 website http://anmaweb.org/AMNS-2016 to find 
more information about the conference along with the list of cultural, 
educational, and historical events in Nepal.


From: Santiago Schnell <schnells@umich.edu>
Date: Sun, Jan 17, 2016 at 8:50 PM
Subject: STEP Program: Molecular & Integrative Physiology, May 31-Aug. 19

The Department of Molecular & Integrative Physiology at the University of 
Michigan is pleased to offer Summer Fellows under the Short Term Education 
Program towards Digestive and Metabolic Physiology to support undergraduate 
students from engineering, computational sciences, mathematics or other 
quantitative backgrounds to apply their expertise to research relevant to 
digestive and metabolic physiology and associated diseases. 

Students currently enrolled at any degree granting university or college 
are eligible to apply, with preference give to those students interested in 
a career in research. Each student will be matched, based on their interests, 
to a laboratory led by a faculty member of the Department of Molecular & 
Integrative Physiology. This collection of laboratories is involved in 
nationally recognized research, in topics such as obesity and diabetes, 
endocrine and metabolic diseases, kidney and urologic diseases, nutrition 
and weight control.

The stipend for 2016 will be $4200 for twelve weeks of full-time work from 
May 31 to August 19. The start and end date of the fellowship may be change 
to accommodate overlap with academic year at home institution, if necessary. 
The laboratory hands-on research is completed with a weekly seminar series 
with presentations on responsible conduct of research, career advice and 
couching, and how loss of physiological regulation leads to digestive and 
metabolic diseases. There will be a research forum at the end of the summer 
in which fellows will present their work, as well as opportunities to attend 
research seminars throughout the summer.

Further details and application materials are available from the fellowship 
website: https://sites.google.com/a/umich.edu/step/home

The deadline for applications is February 15, 2016. This summer fellowship 
program is partially funded by the National Institute of Diabetes and 
Digestive and Kidney Diseases (Grant No. R25 DK088752)

If you have any questions, please do not hesitate to contact the student 
program administrator, Ms. Michele Boggs, at mboggs@umich.edu.


From: Tien, Joseph <jtien@math.ohio-state.edu>
Date: Thu, Jan 14, 2016 at 7:21 PM
Subject: Summer School: Mathematical Modeling..., Ohio, June 13-22

US-Canadian Institutes Epidemiology Summer School: Mathematical Modeling of 
Infectious Disease Spread (June 13-June 22, 2016)

Graduate students from the mathematical and life sciences, public health, 
and related fields are encouraged to apply to the 2016 Graduate Summer School 
on Mathematical Modeling of Infectious Disease Spread, to be held at the 
Mathematical Biosciences Institute in Columbus, Ohio. The program for this 
10-day summer school will feature researchers from the mathematical and 
biological sciences, who will deliver lectures, case study presentations, 
and mentor the school participants in special project groups. The case study 
lectures will focus on public health issues, and will be open to the 
university community. During the summer program each student will work on a 
research project in a team of approximately five participants. Topics to be 
covered include: deterministic and stochastic frameworks for modeling disease 
dynamics; disease dynamics on social networks; metapopulations; host behavior 
and disease evolution; vector-borne diseases; zoonotic diseases; pathogen 
dynamics and co-infection.

The summer school will provide students with broad high-level training in 
Mathematical Biology that is unattainable at most institutions. The school 
will focus on the mathematical modeling of infectious diseases, a field 
that is growing in importance because of the many issues in disease spread 
and control arising from new or newly emerging diseases (e.g., SARS, Ebola, 
West Nile virus), and because new data sources are now available to study 
disease transmission, pathogen evolution, and the impact of the social 
behavior of hosts (e.g., genotyping databases, cell phone networks and air 
travel tickets, social networks). Capitalizing on new data sources to 
understand and control these impacts on disease spread requires detailed 
modeling of interactions amongst pathogens and hosts, the training of 
sophisticated modelers, and the development of new mathematics. This summer 
school will seek to prepare students to study such models in their future 

Apply online: https://mbi.osu.edu/event/?id=1030

Applications for acceptance to the school received before January 31, 2016 
will receive full consideration. There is no tuition charged to summer 
school participants. Financial support for local expenses may be available, 
depending upon availability of funds.

The summer school is co-sponsored by the Mathematical Biosciences Institute 
(MBI, Ohio State), the National Institute for Mathematical and Biological 
Synthesis (NIMBioS, Tennesee ?Knoxville), the Fields Institute (Toronto), 
the Centre for Disease Modelling (CDM, York University), the Centre for 
Applied Mathematics in Bioscience and Medicine (CAMBAM), and the Atlantic 
Association for Research in the Mathematical Sciences (AARMS). The National 
Science Foundation (DMS/NSF) and the Society for Mathematical Biology 
(SMB) have provided additional support.


From: Joshua S. Weitz <jsweitz@gatech.edu>
Date: Thu, Jan 14, 2016 at 1:59 PM
Subject: Workshop: Quantitative Laws..., Como, Italy, June 13-25 

Lake Como Workshop on Quantitative Laws from Physiology to Ecology

Featuring 25+ confirmed speakers, this two-week workshop will communicate 
foundations and advances in research in key cutting-edge areas at the 
interface of statistical physics, nonlinear dynamics, physiology and ecology.

The workshop is divided in two themes, centered on results, discoveries and 
methods in the areas of (Week 1) physiology to ecology and (Week 2) 
interaction structures to collective behavior.

The workshop will provide the necessary methodological tools and perspectives 
to enable a junior researcher to understand and perform cutting-edge research 
in these areas. It will primarily target PhD students and postdocs with a 
physics or mathematics background, but it is open to anyone with background 
in (evolutionary) genomics, (evolutionary) biology, bioinformatics, ecology, 
who is interested in quantitative work.

The lectures / talks will promote sharing of both general knowledge and 
cutting-edge research - with mini-courses and thematic seminar sessions - 
and will create a stimulating environment, facilitating discussions and the 
creation of new collaborations, all in a lake-side setting.

Applications for participation, including travel awards and contributed 
talks are due February 29, 2016:



From: Catherine Crawley <ccrawley@nimbios.org
Date: Fri, Jan 15, 2016 at 3:26 PM
Subject: Workshop: Algebraic Mathematical Biology, NIMBioS, July 25-27

The National Institute for Mathematical and Biological Synthesis (NIMBioS) 
is now accepting applications for its Investigative Workshop, "Discrete and 
Algebraic Mathematical Biology: Research and Education," to be held 
July 25-27, 2016, at NIMBioS.

Co-Organizers: Raina Robeva, Mathematics, Randolph-Macon College, VA; 
Matthew Macauley, Mathematical Sciences, Clemson Univ., SC; and John Jungck, 
Biological Sciences, Center for Bioinformatics and Computational Biology, 
Univ. of Delaware 

For more information about the workshop and a link to the online application 
form, go to http://www.nimbios.org/workshops/WS_mathbio

Participation in the workshop is by application only. Individuals with a 
strong interest in the topic are encouraged to apply, and successful 
applicants will be notified within two weeks of the application deadline. 
If needed, financial support for travel, meals, and lodging is available 
for workshop attendees.


From: Kisdi, Eva <eva.kisdi@helsinki.fi> via helsinkifi.onmicrosoft.com 
Date: Fri, Jan 15, 2016 at 8:36 AM
Subject: Summer school: Structured populations, Finland, August 21-28 

We are pleased to announce the 2016 edition of The Helsinki Summer School on 
Mathematical Ecology and Evolution, an EMS-ESMTB School in Applied 
Mathematics, which will focus on structured populations. The school will be 
held between 21 and 28 August 2016 in Turku, Finland. The core program 
consists of five series of lectures:
Mats Gyllenberg (University of Helsinki): Dynamics of structured populations
Hans Metz (Univ of Leiden): Adaptive dynamics in structured populations
Reinhard Bürger (University of Vienna): Population genetics of spatially 
structured populations
Hisashi Inaba (University of Tokyo): Infectious diseases in structured 
André de Roos (University of Amsterdam): Population and community ecology 
of ontogenetic development
All young researchers working in mathematical ecology can apply from all 
countries, especially from Europe and the Mediterranean. The school is aimed 
at graduate students of mathematics, but we also welcome students of biology 
with sufficient background in mathematics, as well as advanced 
undergraduates and postdocs.
The deadline for applications is 31 January 2016. For more details and 
application, see the school's website at


From: <benitez@bcamath.org>
Date: Thu, Jan 14, 2016 at 1:31 PM
Subject: Workshop: Quantitative Biomedicine for Health and Disease

BCAM is pleased to announce the second workshop on Quantitative Biomedicine
for Health and Disease. The aim of the workshop is to bring together
quantitative researchers of varied background working in biomedical 
sciences. Particular attention will be given to clinical applications.

Confirmed Speakers:
Rafael MOLINA SORIANO (University of Granada)
Iñigo GABILONDO (BioCruces)
Markus DAHLEM (Institut für Theoretische Physik-Technische Univ Berlin)
Paolo BONIFAZI (BioCruces)
Mauro D?AMATO (BioCruces)
Denis DOORLY (Imperial College London)
Alessandro VENEZIANI (Emory)
Daniela CALVETTI (Case Western University)
Iñaki LOPEZ (Cruces Hospital)

Scientific Organizers and Program Chairs:
Sebastiano STRAMAGLIA (University of Bari)
Jesús M. CORTÉS (BioCruces).

The registration fee is 50 Euros (including coffee breaks and lunches).
Inscription is required by email at qbio@bcamath.org

Abstracts (one single .pdf page) can be submitted by January 22.

Further information: http://www.bcamath.org/en/


From: R Eftimie <reftimie@maths.dundee.ac.uk>
Date: Thu, Jan 14, 2016 at 1:07 AM
Subject: PhD Studentship: Mathematical Ecology, Univ of Dundee, UK

PhD Studentship in Mathematical Ecology at the University of Dundee, UK

Deadline for application: 31 January 2016
Studentship expected start date: 1 October 2016
Studentship duration: 4 years

Project title: 
Investigating the effect of noise from Oil & Gas activities on the 
collective behaviour of fish and marine mammals

There is increasing evidence that the wellbeing of marine animals is 
affected by the exposure to underwater sound (noise) that arises from 
activities related to the Oil & Gas (O&G) industry during the exploration, 
development, production and decommissioning phases of the O&G activities. 
In particular, the past 10 years have seen an increase in various 
experimental approaches to test the effects of noise on the wellbeing of 
individual marine animals. On the other hand, various approaches have been 
developed to measure external noise levels associated with O&G activities, 
and actions have been suggested on how to reduce the impact on marine life.
One of the open questions in the field of behavioural marine ecology 
(difficult to be addressed experimentally) is assessing the specific impacts 
of noise associated with O&G industry on the behavioural changes at the 
group level (e.g., persistence or splitting of schools of fish, pods of 
whales, etc.). This is an important aspect to be addressed since the 
survival of some species depends on being in large groups (which help 
individuals against predators, finding food, etc.). The goal of this 
research is to use mathematical modelling (combined with available 
experimental data) to propose hypotheses regarding the effect of O&G noise 
on the inter-individual communication between the members of large marine 
animal aggregations. The research will help increase our understanding of 
the role of man-made noise on the biological mechanisms that disrupt marine 
animal movements and behaviour, and eventually lead to better mitigation 
methods to increase population survival.
Supervisors: Dr. Raluca Eftimie (Mathematics), Prof. Terry Dawson 
(Environmental Sciences)

How to apply:  
Please submit a CV and Cover Letter to Dr. Raluca Eftimie 
(r.a.eftimie@dundee.ac.uk) Informal enquiries can also be directed to 
Dr. Raluca Eftimie.

Eligibility & Criteria Guidance:
The successful candidate will have a background in Mathematics or other 
related disciplines (Physics, Engineering, etc.). Computer programming 
skills (in Matlab, C, etc.) are required. Interest in marine ecology is 
desirable. Candidates must have a minimum 2.1 degree or higher, and hold 
UK citizenship. If you have a 2.2 degree, but have also obtained a masters 
qualification or have equivalent evidence of prior professional practice or 
learning, you are also eligible. Because of NERC (UK) restrictions, the 
full studentships will be available only to UK residents. For complete 
information on students eligibility, please consult the following websites:


From: Vivien Kirk <v.kirk@auckland.ac.nz>
Date: Tue, Jan 19, 2016 at 9:06 PM
Subject: PhD studentship, Dynamical Systems..., Univ of Auckland

A PhD studentship is available in the Department of Mathematics at the 
University of Auckland, for work on a project in dynamical systems and 
mathematical physiology. The project aims to identify the physiological 
mechanisms that underlie the long-period calcium oscillations and waves 
seen in experiments on pancreatic and parotid acinar cells, and involves 
the researchers James Sneyd, Hinke Osinga, and Vivien Kirk at the University 
of Auckland, and Martin Wechselberger at the University of Sydney.
A good background in dynamical systems and scientific programming is 
desirable, as is an interest in mathematical physiology.
Stipend is NZ$27,500 pa (tax free) for three years plus tuition fees. 
Interested candidates should send an email expressing their interest, 
along with a CV and academic record, to Vivien Kirk at v.kirk@auckland.ac.nz
Closing date: 22nd February, 2016


From: Terry, John <J.Terry@exeter.ac.uk>
Date: Mon, Jan 18, 2016 at 3:16 AM
Subject: Lectureship, Mathematical Biology/Medicine, Univ of Exeter

The University of Exeter have an opening for a Lectureship (equivalent to 
Asst Professor) in Mathematical Biology/Medicine. The successful applicant 
will join the Systems Biomedicine Research Group, one of the most rapidly 
growing research groups within the Discipline of Mathematics and Computer 
Science. Comprising 2 Professors, 2 Senior Lecturers, 1 MRC funded Senior 
Research Fellow and 1 Lecturer, the group hosts the EPSRC funded Centre for 
Predictive Modelling in Healthcare and the Wellcome Trust ISSF funded Centre 
for Biomedical Modelling and Analysis. Collectively these activities are 
underpinned by £6M in research funding which supports 16 postdoctoral 
researchers and 10 PhD students. 

The position would suit applicants with a background in dynamical systems 
theory and numerical continuation, complex network analysis, uncertainty 
quantification or parameter inference, who wish to work at the interface 
with biology and/or medicine and who have ambitious plans for growing 
their research profile.

For further details and how to apply please visit: 

The closing date for applications is February 3rd.


Subject: SMBnet Reminders

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