James A. Glazier | |
|---|---|
| Born | June 1962 (age 62) |
| Nationality | USA |
| Alma mater | The University of Chicago |
| Scientific career | |
| Institutions | Indiana University |
| Thesis | Dynamics of Cellular Patterns |
| Academic advisors | Albert Libchaber |
James Alexander Glazier (born June 27, 1962) [1] is a biophysicist and bioengineer, author, and educator best known for his contributions to the field of multiscale modeling, pattern formation, and morphogenesis in biological systems. Glazier has published numerous articles in leading scientific journals, and his work has been widely recognized within the scientific community. [2] He has also been influential in promoting the use of computational modeling and simulation in the study of complex biological phenomena. [3]
James A. Glazier was born in (Cambridge,Massachusetts, on June 27, 1962) to Ira A. Glazier (an economist and demographer) and Elaine A. Glazier (a psychologist and later an entrepreneur). (Need citation) He showed an early interest in science and mathematics, which led him to pursue an undergraduate degree in physics and mathematics from (Harvard College). He later earned his Ph.D. in experimental condensed matter physics from the University of Chicago in 1989, where he worked under the supervision of Prof. Albert J. Libchaber, focusing on chaotic flows in fluids and the coarsening dynamics of liquid foams. [4] While at the University of Chicago, he began a collaboration with Dr. Gary Grest and Dr. David Srolovitz of Exxon Research applying the Potts Model to model the dynamics of foam coarsening. [5] His work on foams [6] led to extensive collaborations with the noted solid-state theorist Prof. Denis Weaire of Trinity College, Dublin. [7] [8]
Following the completion of his Ph.D., Glazier held postdoctoral positions at AT&T Bell Laboratories (1989-1991) where he retrained in experimental developmental neuroscience under Dr. David W. Tank, and then held an NSF/JSPS fellowship (1991-1993) in the Research Institute of Electrical Communication, Tohoku University, Sendai, Japan, where he studied hydra regeneration and, in collaboration with Dr. Francois Graner, developed the Cellular Potts Model (CPM, also known as the Glazier-Graner-Hogeweg model, GGH) formalism for simulating the dynamics of cells in biological tissues. [9] In 1993, he accepted a faculty position in Physics at the University of Notre Dame. He moved to the Department of Physics at Indiana University in 2002, where he established the Biocomplexity Institute to advance interdisciplinary study of biological systems. He has held visiting faculty positions at the University of Western Australia, the University of Grenoble, Tohoku University, the University of California Los Angeles, and the University of California Santa Barbara,
Glazier's research interests lie at the intersection of physics, biology, and computer science, with a focus on understanding the fundamental principles governing the organization and dynamics of living systems. His most notable contributions have been in the area of multiscale modeling of tissues (Virtual Tissues) where he has developed models that have provided insights into a range of biological phenomena, such as morphogenesis, tissue development, vascular development, developmental diseases, including cancer [10] and polycystic kidney disease and toxicology. He has also conducted research on the physics of liquid foams, [11] high-Reynolds number turbulence, on biological ontologies and in microfluidics and biosensors.
Glazier is one of the key developers of CompuCell3D, [12] an open-source software platform for modeling cell behavior in a 3D environment based on the CPM/GGH methodology. CompuCell3D is designed to simulate cell-based biological processes, such as tissue development, morphogenesis, and cellular differentiation. As a professor and researcher, Dr. Glazier has played a significant role in the development and application of CompuCell3D for various biological systems. More recently, with Dr. Enrdre Somogyi [13] and Dr. TJ Sego, he has contributed to the development of the open-source Tissue Forge virtual-tissue simulation environment based on center-model methodologies. His work has contributed to the advancement of computational modeling and simulation techniques in the fields of biophysics, bioengineering, toxicology, and complex systems.
In addition to his research, Glazier has been an active participant in the scientific community. He has served on the editorial boards of Nonlinearity and Bulletin of Mathematical Biology, as well as on numerous grant review panels and advisory committees. He has also been involved in the organization of conferences and workshops aimed at fostering interdisciplinary collaboration among researchers studying complex biological systems and has organized more than 18 summer schools teaching multiscale modeling techniques to a diverse range of students from around the world. He has served as Chair of the Division of Biological Physics of the American Physical Society. In 2020, he co-founded the IMAG/MSM [14] Working Group on Multiscale Modeling and Viral Pandemics, [15] which provides a forum for the application of modeling methodologies to the understanding of infection and immune response. In 2023, with Prof. Tomas Helikar of the University of Nebraska, Lincoln, he co-founded the Global Alliance for Immune Prediction and Intervention, which aims to develop medical Digital Twins to optimize patient-specific medical care. [16] [17]
Throughout his career, James A. Glazier has received numerous accolades for his research achievements, being named a fellow of the Institute of Physics (London), the American Physical Society, [18] and the American Association for the Advancement of Science. [19] His work has been cited extensively in the scientific literature and has inspired many researchers in the fields of biophysics and computational biology. He holds 13 patents in biosensors, microfluidics, drug discovery, and computational modeling.
 | This section of a biography of a living person does not include any references or sources .(October 2023) |
Glazier has lived since 2002 with James Ferguson (citation), an artist, and farmer. He is devoted to baroque opera (he has served on the board of directors of the Boston Early Music Festival) and to travel, with a specific interest in Mongolian archaeology.
Morphogenesis is the biological process that causes a cell, tissue or organism to develop its shape. It is one of three fundamental aspects of developmental biology along with the control of tissue growth and patterning of cellular differentiation.
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Biomechanics is the study of the structure, function and motion of the mechanical aspects of biological systems, at any level from whole organisms to organs, cells and cell organelles, using the methods of mechanics. Biomechanics is a branch of biophysics.
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Mathematical and theoretical biology, or biomathematics, is a branch of biology which employs theoretical analysis, mathematical models and abstractions of living organisms to investigate the principles that govern the structure, development and behavior of the systems, as opposed to experimental biology which deals with the conduction of experiments to test scientific theories. The field is sometimes called mathematical biology or biomathematics to stress the mathematical side, or theoretical biology to stress the biological side. Theoretical biology focuses more on the development of theoretical principles for biology while mathematical biology focuses on the use of mathematical tools to study biological systems, even though the two terms are sometimes interchanged.
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Multiscale modeling or multiscale mathematics is the field of solving problems that have important features at multiple scales of time and/or space. Important problems include multiscale modeling of fluids, solids, polymers, proteins, nucleic acids as well as various physical and chemical phenomena.
CompuCell3D (CC3D) is a three-dimensional C++ and Python software problem solving environment for simulations of biocomplexity problems, integrating multiple mathematical [morphogenesis] models. These include the cellular Potts model (CPM) or Glazier-Graner-Hogeweg model (GGH) which can model cell clustering, growth, division, death, adhesion, and volume and surface area constraints; as well as partial differential equation solvers for modeling reaction–diffusion of external chemical fields and cell type automata for differentiation. By integrating these models CompuCell3D enables modeling of cellular reactions to external chemical fields such as secretion or resorption, and responses such as chemotaxis and haptotaxis.
In computational biology, a Cellular Potts model is a computational model of cells and tissues. It is used to simulate individual and collective cell behavior, tissue morphogenesis and cancer development. CPM describes cells as deformable objects with a certain volume, that can adhere to each other and to the medium in which they live. The formalism can be extended to include cell behaviours such as cell migration, growth and division, and cell signalling. The first CPM was proposed for the simulation of cell sorting by François Graner and James A. Glazier as a modification of a large-Q Potts model. CPM was then popularized by Paulien Hogeweg for studying morphogenesis. Although the model was developed to describe biological cells, it can also be used to model individual parts of a biological cell, or even regions of fluid.
Arieh Warshel is an Israeli-American biochemist and biophysicist. He is a pioneer in computational studies on functional properties of biological molecules, Distinguished Professor of Chemistry and Biochemistry, and holds the Dana and David Dornsife Chair in Chemistry at the University of Southern California. He received the 2013 Nobel Prize in Chemistry, together with Michael Levitt and Martin Karplus for "the development of multiscale models for complex chemical systems".
A cellular model is a mathematical model of aspects of a biological cell, for the purposes of in silico research.
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The Turing pattern is a concept introduced by English mathematician Alan Turing in a 1952 paper titled "The Chemical Basis of Morphogenesis" which describes how patterns in nature, such as stripes and spots, can arise naturally and autonomously from a homogeneous, uniform state. The pattern arises due to Turing instability which in turn arises due to the interplay between differential diffusion of chemical species and chemical reaction. The instability mechanism is unforeseen because a pure diffusion process would be anticipated to have a stabilizing influence on the system.
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Klaus Schulten was a German-American computational biophysicist and the Swanlund Professor of Physics at the University of Illinois at Urbana-Champaign. Schulten used supercomputing techniques to apply theoretical physics to the fields of biomedicine and bioengineering and dynamically model living systems. His mathematical, theoretical, and technological innovations led to key discoveries about the motion of biological cells, sensory processes in vision, animal navigation, light energy harvesting in photosynthesis, and learning in neural networks.
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libRoadRunner is a C/C++ software library that supports simulation of SBML based models.. It uses LLVM to generate extremely high-performance code and is the fastest SBML-based simulator currently available. Its main purpose is for use as a reusable library that can be hosted by other applications, particularly on large compute clusters for doing parameter optimization where performance is critical. It also has a set of Python bindings that allow it to be easily used from Python as well as a set of bindings for Julia.
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