Department of Mathematics

Interdisciplinary Seminar on Mathematical & Computational Modeling

Interdisciplinary Seminar on Mathematical & Computational Modeling

Contact: Dr. Mark Albermalber@ucr.edu 


Upcoming Talks

January 22nd, 2019
2:10 - 3:30 Skye 268

Prof. Douglas J. Tobias, UC Irvine

Title: "Simulation studies of protein interactions and organization in crowded solutions"

Abstract: The cell is a crowded place! For example, the concentration of proteins and nucleic acids in the cytoplasm of E. Coli is > 300 g/L, and eye lens fiber cells contain crystallin proteins at a concentration of ~400 g/L. The nature of the interactions and organization of the macromolecules in such crowded environments is obviously quite different than in typical in vitro experiments and atomistic simulations, which are carried out at orders of magnitude lower concentrations. There are a number of challenges to atomically detailed simulations of biological macromolecules in realistic (i.e., crowded) cellular environments. First and foremost is the necessity of including a large number of macromolecules, which means that the minimal system size is prohibitive to atomistic simulations with explicit solvent. The usual approach to meet this challenge is to employ Brownian dynamics (BD) simulations of atomically detailed, rigid macromolecules in implicit solvent. This approach enables the simulation of ~1,000 macromolecules for ~10-100 microseconds. In this talk, I will describe our efforts to use the energy function employed in BD simulations in Monte Carlo (MC) simulations, which, through clever choices of trial moves, enable much more efficient configurational sampling than BD simulations.  I will also describe how we incorporate conformational flexibility into our MC simulations. Finally, I will present results from our MC simulations of crowded solutions of wild-type and cataract-related variants of eye lens crystallin proteins, which provide molecular-scale insights into the role of altered interprotein interactions in the formation of large-scale aggregates implicated in cataract formation.


Professor Tobias received BS and MS degrees in Chemistry from the University of California, Riverside, in 1984 and 1985, respectively. He received his PhD in Chemistry and Biophysics under the direction of Professor Charles L. Brooks III at Carnegie Mellon University in 1991, where he was a National Institutes of Health pre-doctoral trainee from 1987-1990.  He was a post-doctoral researcher in the lab of Professor Michael Klein in the chemistry department at the University of Pennsylvania from 1991-1995, where he was supported by a National Research Service Award from the National Institutes of Health from 1991-1994.  He was a guest researcher at the National Institute of Standards and Technology from 1995-1997, and he joined the faculty of the Department of Chemistry at the University of California, Irvine, in 1997.  He was promoted to Associate Professor in 2003 and Professor in 2005.

Professor Tobias is a computational chemist.  He uses atomistic simulation techniques based on classical and quantum mechanics to study protein dynamics, solvation, and protein-protein and protein-lipid interactions in aqueous solution and membranes. A substantial portion of his work is devoted to the development and implementation of novel simulation methodology and analysis tools. His current research interests include protein-solvent dynamical coupling, and the biophysics of membranes, ion channel proteins, and structural proteins and water channels in the eye lens.

Professor Tobias is a fellow of the American Association for the Advancement of Science, the American Chemical Society, and the American Physical Society. He was the recipient of the 2014 Theoretical Chemistry Award from the Physical Chemistry Division of the American Chemical Society and the 2017 Soft Matter and Biophysical Chemistry Award from the Royal Society of Chemistry.




Past Talks

December 4th, 2018
2:10 - 3:30 Skye 268

Prof. Mona Eskandari Department of Mechanical Engineering, University of California, Riverside

Title: "Pulmonary Healthcare"

Abstract: Lung disease is the leading cause of death worldwide and yet,pulmonary mechanics and airway obstruction remain drastically understudied.Computational modeling paired with experimental characterization offers an iterative framework for establishing airway mechanics and exploring tissue remodeling due to disease-driven adaptation. Our simulations integrate the theory of finite growth, continuum mechanics, and nonlinear finite element analysis; results rationalize clinical observations and elucidate the complex phenomenon of airway obstruction. Our complementary tissue experiments address the pressing need for understanding the biophysical response of airways, characterizing mechanical and viscoelastic anisotropyand and heterogeneity. Findings inform the first structurally-reinforced constitutive model of proximal and distal bronchi, directly providing the foundation for pulmonary fluid-structure interaction research. This combinatory computational-experimental approach ultimately sets the stage for translational discoveries by enabling predictive modeling, advanced medical diagnostics, and optimized interventions in pulmonary healthcare.

Bio: Mona Eskandari is an Assistant Professor in the Department of Mechanical Engineering (Cooperating Faculty in the Department of Bioengineering, collaborating with the School of Medicine's multidisciplinary BREATHE center) at UC-Riverside.Prior to her postdoctoral fellowship at UC-Berkeley, she received her doctorate and master's degree from Stanford University, and her bachelor’s degree from the University of Arizona, where she was also a Nugent medalist. She was granted the University of California Provost's Engineering Research Fellowship, and was previously named a National Science Foundation Graduate Research Fellow, a DARE Doctoral Fellow,and a Stanford Graduate Science and Engineering Fellow. Her area of expertise is computational modeling and experimental characterization of biological systems,with an emphasis on pulmonary mechanics. Eskandari received the Early Engineering Educator Award from the American Society for Engineering Education for innovative teaching, and the prestigious K. Patricia Cross Future Leaders of Higher Education Award from the Association of American Colleges and Universities.


Nov. 27th, 2018
2:10 - 3:30 Skye 268

Dr. Prof. Maksim Plikus Department of Developmental and Cell Biology Stem Cell Research Center University of California, Irvine

Title:Using math to understand how skin heals itself"

Abstract: Skin is the largest organ in our body and it functions to protect us from a variety of external insults. Being at the forefront of bodily defenses, skin often becomes injured, entering the state of emergency that launches rapid and efficient wound healing response.The latter requires coordinated activation and mobilization of multiple skin cell types, including dormant skin stem cells and resident immune cells.While most of the time, wound healing in mammals, including mice and humans,culminates with the formation of a scar tissue, some animals can heal wounds by regeneration, when both hair follicles and fat cells form anew. Systems Biology approaches are required to properly understand cellular and signaling basis of scaring vs. regeneration in skin wounds. In my talk, I will discuss the state of knowledge in this field and will share how we study wound regeneration with the help of mathematical modeling and bioinformatic analyses.

Bio: Dr. Maksim Plikus completed his PhD and first post-doctoral training at the University of Southern California, working with Dr. Cheng-Ming Chuong.Among other research, his studies identified new mechanism of hair growth coordination by long-range signals. During his second post-doctoral training with Dr. George Cotsarelis at the University of Pennsylvania, Dr. Plikus identified new phenomenon of fat cell regeneration in skin wounds. He joined the University of California Irvine in 2012, where he is currently Associate Professor. His lab continues to study mechanisms of skin homeostasis and regeneration,including with the help of mathematical modeling. Recently his lab published several

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