Long-term behaviors of biochemical systems are described by steady states in deterministic models and stationary distributions in stochastic models. Their analytic solutions can be obtained for limited cases, such as linear or finite-state systems. Interestingly, analytic solutions can be easily obtained when underlying networks have special topologies, called weak reversibility (WR) and zero deficiency (ZD). However, such desired topological conditions do not hold for the majority of cases. Thus, we propose a method of translating networks to have WR and ZD while preserving the original dynamics was proposed. Additionally, we prove necessary conditions for having WR and ZD after translation. Our method provides a valuable tool for analyzing and understanding the long-term behavior of biochemical systems, and we demonstrate its efficacy with several examples.

# Methods for Biological Modeling Subgroup (MFBM)

**Ad hoc subgroup meeting room(reserved for subgroup activities)**:

Senate Chamber in The Ohio Union

###### Jump to:

# Sub-group minisymposia

##### MS01-MFBM-1:

Recent advances in the mathematics of biochemical reaction networks

**Organized by:** Tung Nguyen, Matthew Johnson, Jiaxin Jin

Note: this minisymposia has multiple sessions. The other session is **MS02-MFBM-1**.

**Hyukpyo Hong***Institute for Basic Science (Biomedical Mathematics Group)*

"Network translation allows for revealing long-term dynamics of stochastic reaction networks"**Angelyn Lao***De La Salle University (Department of Mathematics and Statistics)*

"A Reaction Network Analysis of Insulin Signaling"**M. Ali Al-Radhawi***Northeastern University (Department of Electrical and Computer Engineering)*

"Contraction and entrainment in reaction networks"**Jinsu Kim***POSTECH (Mathematics / Mathematical biology)*

"Recent studies about mixing times of stochastically modeled reaction networks"

##### MS01-MFBM-2:

Integration of data and modeling for multiscale biology

**Organized by:** Yuchi Qiu, Heyrim Cho

**Jianhua Xing***University of Pittsburgh (Computational and Systems Biology)*

"Reconstructing cellular dynamics from single cell data"**Aden Forrow***University of Maine (Mathematics and Statistics)*

"Trajectory inference with lineage tracing"**Yuchi Qiu***Michigan State University (Department of Mathematics)*

"Interpretable AIs in data-driven biology: from topological data analysis to multiscale modeling"

##### MS02-MFBM-1:

Recent advances in the mathematics of biochemical reaction networks

**Organized by:** Tung Nguyen, Matthew Johnson, Jiaxin Jin

Note: this minisymposia has multiple sessions. The other session is **MS01-MFBM-1**.

**James Brunner***Los Alamos National Laboratory (Biosciences)*

"Inferring microbial interactions with their environment from genomic and metagenomic data"**Tung Nguyen***Texas A&M University (Department of Mathematics)*

"Absolute concentration robustness in multi-site phosphorylation networks with a bifunctional enzyme"**Jiaxin Jin***The Ohio State University (Mathematics)*

"Weakly reversible deficiency one realizations of polynomial dynamical systems: an algorithmic perspective"**Aidan S. Howells***University of Wisconsin–Madison (Mathematics)*

"Stochastic reaction networks within interacting compartments"

##### MS03-MFBM-1:

Stochastic methods for biochemical reaction networks

**Organized by:** Wasiur KhudaBukhsh, Hye-Won Kang

Note: this minisymposia has multiple sessions. The other session is **MS04-MFBM-1**.

**Grzegorz A. Rempala***The Ohio State University (Biostatistics)*

"Agent-based, aggregated dynamics for chemical reaction networks"**Hye-Won Kang***University of Maryland, Baltimore County (Department of Mathematics and Statistics)*

"Stochastic oscillations in the enzyme-catalyzed chemical reaction network in glycolysis"**Yi Fu***University of California, San Diego (Bioinformatics and Systems Biology PhD Program)*

"Comparison Theorems for Stochastic Chemical Reaction Networks"**Arnab Ganguly***Louisiana State University (Mathematics)*

"Statistical inference of stochastic differential equations with applications to biochemical reactions"

##### MS03-MFBM-2:

Inference, analysis, and control of Boolean network models

**Organized by:** David Murrugarra

**Elena Dimitrova***California Polytechinc State University, San Luis Obispo (Mathematics)*

"A unified approach to reverse engineering and data selection for unique network identification"**Brandilyn Stigler***Southern Methodist University (Mathematics)*

"Computational Algebraic Methods for Boolean Network Modeling"**Claus Kadelka***Iowa State University (Department of Mathematics)*

"A modular design of gene regulatory networks emerges naturally in response to an evolutionary multi-objective optimization problem"**Daniel R. Plaugher***University of Kentucky (Department of Toxicology and Cancer Biology)*

"Phenotype control techniques for gene regulatory networks"

##### MS04-MFBM-1:

Stochastic methods for biochemical reaction networks

**Organized by:** Wasiur KhudaBukhsh, Hye-Won Kang

Note: this minisymposia has multiple sessions. The other session is **MS03-MFBM-1**.

**Wasiur R. KhudaBukhsh***University of Nottingham (School of Mathematical Sciences)*

"Multiscale approximations for a simple transfection process"**Ruth Baker***University of Oxford (Mathematical Institute)*

"Efficient approaches for simulating and calibrating stochastic models of biological processes"**Jae Kyoung Kim***KAIST (Mathematical Sciences)*

"Inference of non-Markovian systems from cell signaling to infectious diseases"**Boseung Choi & Eunjin Eom***Korea University (Division of Big Data Science; Department of Economics Statistics)*

"A Bayesian model for the relationship SARS-CoV-2 wastewater and community-wide seroprevalence with mutation and vaccination effect"

##### MS05-MFBM-1:

Data-driven methods for biological modeling

**Organized by:** John Nardini, Erica Rutter, Kevin Flores

**Natalia Kravtsova***The Ohio State University (Department of Mathematics)*

"Scalable Gromov-Wasserstein based comparison of biological time series"**Yordan P. Raykov***University of Nottingham (Statistics and Probability)*

"Digital disease progression biomarkers for Parkinson's disease: algorithms for passive monitoring"

##### MS06-MFBM-1:

Algebra, Combinatorics, and Topology in Modern Biology

**Organized by:** Daniel A. Cruz,Margherita Maria Ferrari

**Lina Fajardo Gomez***University of South Florida (Mathematics)*

"Homology for Directed Graphs with Applications to DNA Recombination"**Puttipong Pongtanapaisan***Arizona State University (Mathematics and statistics)*

"On the scarcity of split links spanning a lattice tube"**Caitlin Lienkaemper***Boston University (Department of Mathematics and Statistics)*

"Combinatorial coexpression in mosquito olfaction"**Radmila Sazdanovic***NC State University (Mathematics)*

"Categorified chromosome aberration model"**Margherita Maria Ferrari***University of Manitoba (Department of Mathematics)*

"Graph theory for DNA self-assembly"

##### MS06-MFBM-2:

Data-driven multiscale modeling of cancer

**Organized by:** Heber Rocha, John Metzcar, Paul Macklin

**Alexander Browning***University of Oxford (Mathematical Institute)*

"Drawing biological insight from non-identifiabile models of tumour growth using simple surrogates"**Jeanette Johnson***Johns Hopkins University (Immunology)*

"Integrating Omics Data and Agent-Based Models for Comprehensive Digital Biology"**Adam MacLean***University of Southern California (Department of Quantitative and Computational Biology)*

"Learning gene regulatory networks that control cell state transitions from multi-modal single-cell genomics"**Matthew Simpson***Queensland University of Technology (School of Mathematical Sciences)*

"A stochastic mathematical model of 4D tumour spheroids with real-time fluorescent cell cycle labelling"

##### MS08-MFBM-1:

Stochastic Methods in Oncology and Population Dynamics

**Organized by:** Linh Huynh, Deena Schmidt

**Heyrim Cho***University of California Riverside (Mathematics)*

"Modeling of CAR T-cell and neural stem cell therapy for brain cancer"**Alexandru Hening***Texas A&M (Mathematics)*

"Population dynamics under random switching"**Khanh Ngoc Dinh***Columbia University (Irving Institute for Cancer Dynamics)*

"Modeling and simulation of cancer evolution in bulk and single-cell DNA-sequencing data"**James MacLaurin***New Jersey Institute of Technology (Mathematics)*

"From blips to puffs: estimating the probability of noise-induced calcium waves"

# Sub-group contributed talks

##### CT01-MFBM-1:

MFBM Subgroup Contributed Talks

**Connor McShaffrey***Indiana University Bloomington*

"Decomposing Viability Space"**Holly Huber***University of Southern California*

"Systematic Bayesian Posterior Analysis Facilitates Hypothesis Formation and Guides Investigation of Pancreatic Beta Cell Signaling"**Nathaniel Linden***University of California San Diego*

"Multimodel modeling for blood glucose and insulin measurements in diabetes"**Robert DeJaco***National Institute of Standards and Technology*

"Reducing Bias and Quantifying Uncertainty in Fluorescence Produced By PCR"

##### CT02-MFBM-1:

MFBM Subgroup Contributed Talks

**Anna Konstorum***Institute for Defense Analyses*

"A decomposition as a model: extracting mechanistic information from high-throughput time-course data using tensor dictionary learning"**Dewayne A. Dixon***Howard University*

"Core Epigenetic Module Biomarkers among Various PTSD Subtypes"**Heber L Rocha***Indiana University*

"Multiscale Modeling and Data Assimilation: A Path to Personalized Medicine"**Hyun Kim***Institute for basic science*

"Enhancing dimensionality reduction in single-cell RNA sequencing: a novel tool for improved preprocessing and noise filtering"

##### CT03-MFBM-1:

MFBM Subgroup Contributed Talks

**Hyeontae Jo***Institute for Basic Science (IBS)*

"Density Physics-Informed Neural Network infers an arbitrary density distribution for non-Markovian system"**Luigi Frunzo***University of Naples Federico II*

"Mathematical modelling of phototrophic-heterotrophic biofilm system"**Samantha Linn***University of Utah*

"First passage times under frequent stochastic resetting"**Silvia Berra***University of Genova, Italy*

"Drug dosage in cancer: a mathematical approach for computing steady states of chemical reaction networks"

##### CT03-MFBM-2:

MFBM Subgroup Contributed Talks

**Jordan Collignon***University of California, Merced*

"[PSI]-CIC: A Deep-Learning Pipeline for the Annotation of Sectored Saccharomyces cerevisiae Colonies"**Md Masud Rana***University of Kentucky*

"Differential geometry and graph theory-based machine-learning model for drug design"**Theo Loureaux***University of California Merced*

"Automating the Generation of Synthetic Training Data for Biological Image Segmentation"

# Sub-group poster presentations

##### MFBM Posters

**MFBM-01**

**Ahmed Fathi**

*University of Naples Federico II, Naples, Italy*

Poster ID: MFBM-01 (Session: PS01)

"An upscaled model of heavy metal biosorption in homogeneous porous media"

**MFBM-02**

**Alessandro Maria Selvitella**

*Purdue University Fort Wayne*

Poster ID: MFBM-02 (Session: PS01)

"On the variability of human leg stiffness across strides during running gait and some consequences for the analysis of kinematic and kinetic data"

**MFBM-03**

**ANUPAM KUMAR PANDEY**

*Indian Institute of Technology (Banaras Hindu University), Varanasi*

Poster ID: MFBM-03 (Session: PS01)

"Oesophageal catheterisation under the influence of dilating amplitude with peristaltically driven Newtonian fluid: A mathematical model"

**MFBM-04**

**Ari Barnett (Roldan)**

*Moffitt Cancer Center*

Poster ID: MFBM-04 (Session: PS01)

"Approaches for Dealing with Data Disparity and Complex Dynamics"

**MFBM-05**

**Candan Celik**

*Institute for Basic Science*

Poster ID: MFBM-05 (Session: PS01)

"Reducing gene expression noise: The role of RNA stem-loops in translation regulation"

**MFBM-06**

**Dongju Lim**

*KAIST*

Poster ID: MFBM-06 (Session: PS01)

"Mood Prediction for Bipolar Disorder Patient with Sleep Pattern Information"

**MFBM-07**

**Dylan T. Casey**

*University of Vermont, Burlington, VT*

Poster ID: MFBM-07 (Session: PS01)

"An agent-based model of fibrosis on lung architecture"

**MFBM-08**

**Juliano Ferrari Gianlupi**

*Indiana University*

Poster ID: MFBM-08 (Session: PS01)

"PhenoCellPy: A Python package for biological cell behavior modeling"

**MFBM-09**

**Megan Haase**

*University of Virginia*

Poster ID: MFBM-09 (Session: PS01)

"A Cellular Potts Model of skeletal muscle regeneration to reveal novel interventions that improve recovery from muscle injury"

**MFBM-10**

**Randy Heiland**

*Indiana University*

Poster ID: MFBM-10 (Session: PS01)

"PhysiCell Studio: a graphical tool to create, execute, and visualize a multicellular model"

**MFBM-11**

**Rholee Xu**

*Worcester Polytechnic Institute*

Poster ID: MFBM-11 (Session: PS01)

"Experimental measurement of elastic moduli in the moss Physcomitrium patens informs modeling of plant cell tip growth"

**MFBM-12**

**Thomas Dombrowski**

*Moffitt Cancer Center*

Poster ID: MFBM-12 (Session: PS01)

"Tumor-immune ecosystem dynamics exploration via a high-resolution agent-based model"

**MFBM-13**

**Yun Min Song**

*KAIST*

Poster ID: MFBM-13 (Session: PS01)

"Noisy delay denoises biochemical oscillators"

**MFBM-14**

**Xiaojun Wu**

*University of Southern California*

Poster ID: MFBM-14 (Session: PS01)

"Single-cell Ca2+ parameter inference reveals how transcriptional states inform dynamic cell responses"

**MFBM-01**

**Anna-Dorothea Heller**

*Max Planck Institute of Colloids and Interfaces, Potsdam, Germany*

Poster ID: MFBM-01 (Session: PS02)

"A stochastic Cellular Automaton Model to simulate Bone Remodeling"

**MFBM-02**

**Brock Sherlock**

*University of New South Wales*

Poster ID: MFBM-02 (Session: PS02)

"An Algorithmic Approach for Constraining Stochastic Models with Multiple Data Sets"

**MFBM-03**

**Eduardo A. Chacin Ruiz**

*University at Buffalo, The State University of New York, Buffalo, NY*

Poster ID: MFBM-03 (Session: PS02)

"Mathematical Modeling of Drug Release from Bi-Layered Drug Delivery Systems in the Eye"

**MFBM-04**

**Eui Min Jeong**

*Institute for Basic Science (IBS)*

Poster ID: MFBM-04 (Session: PS02)

"Combined multiple transcriptional repression mechanisms generate ultrasensitivity and robust oscillations"

**MFBM-05**

**Farjana Tasnim Mukta**

*University of Kentucky*

Poster ID: MFBM-05 (Session: PS02)

"An Extended Atom Type System for Algebraic Graph-Based Machine Learning Model in Drug Design"

**MFBM-06**

**Furkan Kurtoglu**

*Indiana University*

Poster ID: MFBM-06 (Session: PS02)

"Multiscale Agent-Based Modeling of Metabolic Crosstalk Between Colorectal Cancer Cells and Cancer-Associated Fibroblasts"

**MFBM-07**

**Jabia M. Chowdhury**

*University at Buffalo, The State University of New York, Buffalo, NY*

Poster ID: MFBM-07 (Session: PS02)

"Computational Simulation of Pharmacokinetic Modeling of Drug Bevacizumab in AMD Treatment"

**MFBM-08**

**Jnanajyoti Bhaumik**

*SUNY Buffalo*

Poster ID: MFBM-08 (Session: PS02)

"Fixation dynamics for switching networks"

**MFBM-09**

**Joel Vanin**

*Indiana University Bloomington*

Poster ID: MFBM-09 (Session: PS02)

"Towards a virtual cornea - an agent-based model to study interactions between the cells and layers of the cornea under homeostasis and following chemical exposure."

**MFBM-10**

**Liam D. O'Brien**

*The Ohio State University*

Poster ID: MFBM-10 (Session: PS02)

"Changes in Approximate Symmetries of a Parametrized Turing Pattern"

**MFBM-11**

**Mohammad Nooranidoost**

*Florida State University*

Poster ID: MFBM-11 (Session: PS02)

"Modeling Biofilm Spatio-temporal Organization as a Viscoelastic Gel-mix"

**MFBM-12**

**Nicholas O. Glover**

*University at Buffalo, The State University of New York, Buffalo, NY*

Poster ID: MFBM-12 (Session: PS02)

"Simulating solute transport through the kidney glomerulus using FEBio"

**MFBM-13**

**Richard C. Windecker, PhD**

*N/A (retired from Bell Labs)*

Poster ID: MFBM-13 (Session: PS02)

"An Agent-Based Model for Step Lengths in a Random Walk"

**MFBM-14**

**Saikanth Ratnavale**

*University of Notre Dame*

Poster ID: MFBM-14 (Session: PS02)

"Optimal controls of the mosquito-borne disease, Dengue with vaccination and control measures"

**MFBM-15**

**Torkel Loman**

*Massachusetts Institute of Technology*

Poster ID: MFBM-15 (Session: PS02)

"Catalyst: Fast Biochemical Modeling with Julia"

**MFBM-16**

**Zainab Almutawa**

*University of Maryland Baltimore County*

Poster ID: MFBM-16 (Session: PS02)

"Switching off activity in minimal three-cell topologies of coupled heterogenous beta cells"

**MFBM-17**

**Caroline Tatsuoka**

*The Ohio State University*

Poster ID: MFBM-17 (Session: PS02)

"Data Driven Modeling of Biological Systems with Deep Neural Networks"

**MFBM-18**

**Shawn Means**

*University of Auckland*

Poster ID: MFBM-18 (Session: PS02)

"Reduction of order for uterine smooth muscle cell model: Relevance and Reproducability"

**MFBM-19**

**Dae Wook Kim**

*University of Michigan*

Poster ID: MFBM-19 (Session: PS02)

"Wearable data assimilation to estimate the circadian phase"