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The main long-term goal of the UC Riverside Interdisciplinary Center for Quantitative Modeling in Biology (ICQMB) is to develop comprehensive predictive quantitative models of complex biological systems. All projects at this center combine quantitative experiments, novel image analysis, modeling and statistical approaches, and build upon the mutually complementary strength of the researchers at UC Riverside with support from collaborators at other institutions.

Upcoming Talks

March 9th, 2020
Skye Hall 268

11:00 - 11:50 a.m.

Title: Mechanical Forces on Immune Receptors

Jun Allard


Dr. Jun Allard, Department of Mathematics, University of California, Irvine

https://allardlab.com/

Abstract: Cells receive information through receptors (molecules on their surface) that bind to ligands (external molecules that carry information). An important class of receptors, including the T-cell receptor, bind to ligands that are anchored to the surfaces of other cells. The T-cell receptors themselves are important since they are the site of immunological decision-making, specifically whether or not to mount an immune response against a particular pathogen. Since the 1990s, the presence of the other surface has been speculated to imply forces on the receptor (unlike for receptors where the ligand is soluble), but the small, crowded, noisy environment of cell biology has made these forces challenging to observe experimentally.

Here we present our ongoing efforts to understand these forces at the nanometer scale using mathematical models.  First, we estimate forces and how they influence the T-cell receptor. We find that the force alters the information processing being done by this receptor by endowing the system with nonlinearities, thereby influencing immunological decision making. Second, we study the dynamics of surface molecules undergoing simple Brownian motion. While the equilibrium problem is straightforward, the dynamics problem hints at roles for non-receptor surface molecules and surface’s spatial heterogeneity. Third, we study the thin layer of water separating the two cell surfaces by developing a large-scale computational framework to solve the fluid dynamics problem of two soft, thermally-undulating membranes. Taken together, our work is revealing that forces on receptors lead to nonlinear and sometimes counterintuitive dynamics, and influence how cells process information to perform their biological function.

Bio: Dr. Jun Allard is an associate professor in the Department of Mathematics and Department of Physics & Astronomy at the University of California, Irvine. He also affiliates with the Center for Complex Biological Systems, the NSF-Simons Center for Multiscale Cell Fate Research,and the Chemical and Materials Physics (ChaMP) program at University of California Irvine. He joined UC Irvine in July 2013. Earlier, he was a post-doctoral fellow at UC Davis, where he worked on cytoskeletal dynamics and cell motility. He obtained his Ph.D. in applied mathematics from University of British Columbia in 2011.

 

Center News

Dr. Russell Rockne Appointed Adjunct Assistant Professor in the Department of Mathematics, UC Riverside

Russell Rockne


Dr. Russell Rockne from the City of Hope was appointed Adjunct Assistant Professor in the Department of Mathematics, UC Riverside: https://www.cityofhope.org/people/rockne-russell He is an Assistant Professor in the Department of Computational and Quantitative Medicine within Beckman Research Institute of City of Hope. He also serves as director of the Division of Mathematical Oncology, with the goal of translating mathematics, physics and evolution-based research to clinical care. The division, a part of Irell & Manella Graduate School of Biological Sciences and the Beckman Research Institute of the City of Hope, uniquely combines clinical care, scientific  research and mathematical expertise to enhance the overall understanding of cancer development, growth, evolution and reaction to treatment. This work ultimately helps the care team to predict, control and thwart malignancy on both a global scale by improving evidence-based standards of care and an individual level by personalizing treatment using quantifiable patient and disease factors.

 

The Center is Co-Sponsoring Three Conferences through 2021

1. 9th Annual SoCal System Biology Conference to be held at UCR on February 1, 2020: https://icqmb.ucr.edu/9th-annual-southern-california-regional-systems-biology-conference

2. Dimitrios Morikis Memorial Symposium to be held at UCR on February 10, 2020: https://morikis-symposium.engr.ucr.edu/

3. 2021 Annual Society for Mathematical Biology Meeting to be held at UCR from June 13-17, 2021. This year it will be held in Germany. https://www.smb.org/meetings/

 

DOE Supported Interdisciplinary Collaborative Project at UCR, PNNL and ORNL

Dr. Alber is a co-PI on just awarded three year (9/1/2019-8/31/2022) Department of Energy grant titled: "Elucidating Principles of Bacterial-Fungal Interactions" with total budget of $2,246,000 and with $556,229 for the subaward to UCR.

Interdisciplinary Team includes:

PI: William Cannon, Senior Scientist at the Pacific Northwest National Laboratory and Adjunct Professor, Department of Mathematics, UC Riverside

Co-PI: Mark Alber, Distinguished Professor, Department of Mathematics, UC Riverside

Co-PI: Dale A Pelletier, Senior Staff Scientist in the Biosciences Division at Oak Ridge National Laboratory (ORNL)

Co-PI: Jessy Labbé, Staff Researcher, lead of the Fungal Systems Genetics and Biology Lab in the Biosciences Division at Oak Ridge National Laboratory (ORNL)

Title: Elucidating Principles of Bacterial-Fungal Interactions

Abstract: In comparison to bacterial-bacterial interactions, there is very little known about bacterial-fungal interactions even though these interactions are thought to be fundamentally important to DOE missions in sustainability, crop biofuel development and biosystem design. In biofuel crops, many crop root systems live in mutualistic symbiosis with fungi and bacteria. Mycorrhiza helper bacteria (MHB) increase host root colonization by mycorrhizal fungi, which in turn act as a micro-root system to provide the plant with soil nutrients. Recent work on the Populus root microbiome has determined that the interactions between the mycorrhizal fungus Laccaria bicolor and the bacterium, Pseudomonas fluorescens are key to the fitness of the plant. These organisms, Laccaria and P. fluorescens, are the focus of this project to use combined mathematical and computational modeling and experiments to understand fundamental principles of interactions between fungi and bacteria from the perspective of material exchange and energetics, and how material and energetics are linked in inter- and intra-microbial subsystems.

 

Integrating Machine Learning and Multiscale Modeling Position Paper

Integrating Machine Learning and Multiscale Modeling https://arxiv.org/abs/1910.01258 to be discussed at the Conference to be held at NIH, Bethesda, MD, from October 24-25:

https://www.imagwiki.nibib.nih.gov/msm-consortium/2019-ml-msm

https://www.imagwiki.nibib.nih.gov/msm-consortium/agenda

 

AMS at UC Riverside - 2019

We invite you to participate in the American Mathematical Society (AMS) Fall Western Sectional Meeting to be held at the University of California, Riverside, from November 9-10, 2019 (Saturday - Sunday):

http://www.ams.org/meetings/sectional/2266_timetable.html

In particular, the Meeting will include three Special Sessions on applications to biology as well as the Special Session of the Association for Women in Mathematics (AWM).

 

The 2nd Annual Conference on Quantitative Approaches in Biology will be held October 4-5, 2019 at Northwestern University

This conference is a two-day event that includes a range of activities to stimulate the cross-fertilization of ideas, including guest speaker talks, lightning talks, poster sessions, an undergraduate research competition, a reception, and plenty of networking opportunities.

SPEAKERS Day 1 – October 4, 2019

Hana El-Samad, University of California-San Francisco

Daniel Fisher, Stanford University

Christine Heitsch, Georgia Tech

Madhav Mani, Northwestern University

Andy Oates, L’Ecole Polytechnique Fédérale de Lausanne

Day 2 – October 5, 2019

Nicole Creanza, Vanderbilt University

James Lee, University of Illinois-Chicago

Srividya Iyer-Biswas, Purdue University

Xin Li & Dave Shihai Zhao, University of Illinois-Urbana Champaign

Christian Petersen, Northwestern University

Jeremiah Zartman, University of Notre Dame

Register Here

 

Recent Special Issue of the the Bulletin of Mathematical Biology Includes Papers by Participants of the Conference Held at UC Riverside in 2017

Special Issue on Multiscale Modelling of Tissue Growth and Shape of the Bulletin of Mathematical Biology, Volume 81, Issue 8, August 2019: 3214-3218, doi: 10.1007/s11538-019-00649-2 https://link.springer.com/journal/11538/81/8/page/1 Issue Editors: Mark Alber, Christophe Godin, Philip Maini, Roeland Merks, Eric Mjolsness Introduction: https://link.springer.com/article/10.1007/s11538-019-00649-2

This Special Issue consists of contributions from participants of three workshops with similar focus held in 2016–17: “Modelling of Tissue Growth and Form” held from March 6 to March 10, 2017, at the NSF Mathematical Biology Institute (MBI), Columbus, OH, USA, “Multi-scale Modeling of Complex Systems in Developmental and Plant Biology” held on December 15, 2017, at the Interdisciplinary Center for Quantitative Modeling in Biology, University of California, Riverside, CA, USA, “Computing a Tissue: Modeling Multicellular Systems” at the 15th European Conference on Computational Biology held from September 3 to September 7, 2016, at The Hague, Netherlands. The Special Issue combines papers on recent advances in the field with review articles discussing in detail some open problems. Contributors were asked to describe the recent results on the application of the very latest mathematical and computational modeling and experimental approaches used for studying problems in morphogenesis and growth of plants and animals.

 

Dr. William Cannon Appointed Adjunct Professor in the Department of Mathematics, UC Riverside

William Cannon

Dr. William Cannon from the Pacific Northwest National Laboratory (PNNL) was appointed Adjunct Professor in the Department of Mathematics, UC Riverside: https://www.pnnl.gov/science/staff/staff_info.asp?staff_num=7055

Dr. Cannon's Research Interests include: Computational biophysics, biochemistry and proteomics; Modeling and simulation including deterministic and stochastic simulation of metabolism; simulations of state; microbial metabolism; statistics, statistical mechanics and statistical proteomics data analysis; Cloud computing and high performance.

Dr. Cannon is author of more than 50 technical publications in modeling and simulation, data analysis and proteomics. His graduate work was in statistical thermodynamics in the laboratory of J. Andrew McCammon studying molecular recognition proteins using molecular dynamics and Monte Carlo methods. His graduate work was in the laboratory of Steven J. Benkovic where he worked in both experimental and computational enzymology. Before joining PNNL, Dr. Cannon spent time at Monsanto working on high-throughput transcriptome data analysis and network inference. Since joining PNNL, Dr. Cannon has worked on statistical methods for integrating proteomics data with models, the use of supercomputers to maximize the identification of peptides and proteins from high throughput mass spectrometry assays, and the modeling and simulation of metabolic pathways. Researchgate: www.researchgate.net/profile/William_Cannon2

 

Samuel Britton of UCR Math D.O.E. Office of Science Graduate Student Fellowship

Samuel Britton

Graduate student Samuel Britton in Mathematics Department has been awarded the U.S. Department of Energy (DOE) Office of Science Graduate Student (SCGSR ) Fellowship to conduct research on the collaborative project at the Pacific Northwest National Laboratory (PNNL) titled “Data integration and multi-scale computational model of metabolism”. He will be co-advised on this project by Dr. William Cannon (PNNL) and Dr. Mark Alber (UCR).

The SCGSR Award Notification indicates that: "The selection of Samuel Britton for the SCGSR award is in recognition of outstanding academic accomplishments and the merit of the SCGSR research proposal, and reflects Samuel Britton’s potential to advance the Ph.D. studies and make important contributions to the mission of the DOE Office of Science".