Mark Alber
Department of Mathematics
University of California, Riverside
https://mathdept.ucr.edu/faculty/alber.html
Dr. Alber’s group is working on several interdisciplinary projects combining multi-scale modeling and experimentation. Project on Combined Modeling and Experimental Study of the Mechanisms of Growth Patterns in Stem Cell Homeostasis in Plants aims to understand how mechanical connections among cells and chemical signals between them collaborate to control the growth, sell-organization and differentiation of stem cells during plant growth. Mathematical and computer models will allow researchers to perform virtual experiments that are currently impossible in the lab. Coupled with live imaging experiments and new image analysis methods, these experiments will yield insights into biological mechanisms governing organ formation in plants and animals and development of cancer in epithelial cell layers of the colon.
Another collaborative project with University of Pennsylvania School of Medicine is on multi-scale modeling and empirical study of a mechanism limiting blood clot growth. Thrombosis is a major cause of death in the developed world and results from the growth of thrombi (blood clots forming within blood vessels) that restricts blood flow to vital organs. The project integrates multi-scale modeling and experiments to examine novel hypothesis related to the role of fibrin networks in processes halting thrombus growth. This will help physicians to estimate risk of thrombotic disease for an individual patient by identifying critical values of parameters of processes regulating thrombogenesis.
Selected publications:
1. Samuel Britton, Oleg Kim, Francesco Pancaldi, Zhiliang Xu, Rustem I. Litvinov, John W.Weisel, Mark Alber [2019], Contribution of nascent cohesive fiber-fiber interactions to the non-linear elasticity of fibrin networks under tensile load, Acta Biomaterialia 2019 May 30. pii: S1742-7061(19)30395-2. doi: 10.1016/j.actbio.2019.05.068. [Epub ahead of print].
2. Banwarth-Kuhn M., Nematbakhsh A., Rodriguez KW., Snipes S., Rasmussen CG., Reddy GV., Alber M. [2018], Cell-Based Model of the Generation and Maintenance of the Shape and Structure of the Multilayered Shoot Apical Meristem of Arabidopsis thaliana. Bull. Math. Biol. 2018 Dec 14. doi: 10.1007/s11538-018-00547-z. [Epub ahead of print]
3. Oleg V. Kim, Rustem I. Litvinov, Mark S. Alber and John W. Weisel [2017], Quantitative Structural Mechanobiology of Platelet-Driven Blood Clot Contraction, Nature Communications 8: 1274 (authors for correspondence: J.W. Weisel and M. Alber).
Kurt E. Anderson
Department of Evolution, Ecology, and Organismal Biology
University of California, Riverside
https://www.kurteandersonecology.com/
Dr. Andersen is a quantitative ecologist with interests in the intersection of theoretical, empirical, and applied ecology. He is particularly interested in how ecological systems respond to environmental variation, both natural and human-driven. Current Anderson's lab projects include examining the relationship between spatial network structure and stability of food webs, testing how dendritic river structure influences the temporal stability of freshwater ecological communities at multiple spatial scales, and developing conservation tools for threatened species in the Santa Ana river, an urban, effluent-dominated system.
John Barton
Department of Physics
University of California, Riverside
John Barton is interested in the phenomenology of evolution and the immune system. What forces guide the evolution of viruses and other pathogens, and how does the immune system effectively respond to them? His research emphasizes data and measurement: how can we learn about these processes from available data, and how can we make predictions that can be tested experimentally? The ultimate goal of this work is to help improve the ways that we prevent and treat disease.
Giulia Palermo
Department of Bioengineering
University of California, Riverside
The Palermo research group is focused on the development and applications of molecular dynamics simulations and mixed quantum mechanics/molecular mechanics (QM/MM) methods to study the molecular basis of gene regulation, chromatin structure and dynamics, enzymatic function and ribozyme catalysis. The lab expertise also includes emerging cryo-electron microscopy (cryo-EM) processing methods. Major accomplishments concern the study of the mechanism of action of the CRISPR-Cas9 system, allosteric pathways, catalytic mechanisms in DNA/RNA processing enzymes, membrane proteins and chromatin structures. The lab works in close collaboration with experimental scientists, providing validation to computations.
Giulia Palermo is a native of Italy where she earned her PhD in 2013 from the Italian Institute of Technology. She has been an early post-doctoral scientist in the group of Prof. Ursula Rothlisberger at the Swiss Federal Institute of Technology (EPFL), where she earned expertise in ab-initio Molecular Dynamics. In 2016, she has been awarded a Swiss National Science Foundation (NSF) post-doctoral fellowship to join the group of Prof. J. Andrew McCammon at the University of California San Diego, where she specialised in novel multiscale methods enabling the study of increasingly realistic biological systems.
Selected Publications:
1. C. G. Ricci, J. S. Chen, Y. Miao, M. Jinek, J. A. Doudna, J. A. McCammon and G. Palermo.† Deciphering Off-target Effects in CRISPR-Cas9 through Accelerated Molecular Dynamics. ACS Cent. Sci. 2019, in press
2. L. Casalino, G. Palermo, A. Spinello, U. Rothlisberger and A. Magistrato. All-Atom Simulations Disentangle the Functional Dynamics Underlying Gene Maturation in the Intron Lariat Spliceosome. Proc. Natl. Acad. Sci. USA 2018, 115, 6584-6589.
3. G. Palermo,† C. G. Ricci, A. Fernando, R. Basak, M. Jinek, I. Rivalta, V. S. Batista and J. A. McCammon PAM-induced allostery activates CRISPR-Cas9. J. Am. Chem. Soc. 2017, 139, 16028–16031. Journal Cover Art. Featured in the JACS 2018 Young Investigators Virtual Issue.
4. G. Palermo, Y. Miao, R. C. Walker, M. Jinek and J. A. McCammon. CRISPR-Cas9 conformational activation as elucidated from enhanced molecular simulations. Proc. Natl. Acad. Sci. USA. 2017, 114, 7260–7265.
5. L. Casalino, G. Palermo, U. Rothlisberger and A. Magistrato. Who Activates the Nucleophile in Ribozyme Catalysis? An Answer from the Splicing Mechanism of Group II Introns. J. Am. Chem. Soc. 2016, 138, 10374–10377. Journal Cover Art.
6. G. Palermo, A. Cavalli, M. L. Klein, M. Alfonso Prieto, M. Dal Peraro and M. De Vivo. Catalytic metal ions and enzymatic processing of DNA and RNA. Acc. Chem. Res. 2015, 48, 220–228.
Tamar Shinar
Department of Computer Science & Engineering
University of California, Riverside
https://www.cs.ucr.edu/~shinar
Research interests: Tamar Shinar's research interests include modeling and simulation of fluid-mediated cytoskeletal phenomena, fluid-structure interaction, and physics-based animation.
More to be posted soon.
Qixuan Wang
Department of Mathematics
University of California, Riverside
https://mathdept.ucr.edu/faculty/qwang.html
Dr. Wang’s research area is mathematical biology with main focuses on multi-scale modeling of complex developmental systems. She develops new mathematical models and computational tools to address questions in developmental systems. In particular, she uses mammalian hair follicles as a model system and develop multi-scale models to investigate the underlying control mechanisms of follicle growth and regeneration, the interplay between bio-chemistry and bio-mechanics in follicle development, and the communications among follicles which lead to coordinated follicle growth in different skin domains. She is also interested in developing computational methods and applying analysis in swimming micro-organisms in viscous flows. To answer questions from life sciences, she uses and develops a wide variety of tools including stochastic differential equations, dynamical system, scientific computing, asymptotic analysis and complex analysis.