Welcome to the Cox Group Web page!

We carry out research on theoretical biological physics, currently focusing on

• Self-assembly of beta solenoid proteins and design and development of decoy proteins (that imitate receptors on human cells and can substitute for antibodies) for applications to detection of and protection from viral threats in collaboration with Prof. Javier Arsuaga, Prof. Mariel Vazquez, and Prof. Victor Muñoz and via startup company Protein Architects Corporation
• Modeling how degradation by neurodegenerative diseases affects the neural networks involved in sensing (olfaction and auditory localization) and navigation (grid cells).
• Modeling of the normal function of short term memory and navigation via grid cells, head direction cells, and place cells in the human brain.

News:

May, 2023 – “Using machine learning to detect coronaviruses potentially infectious to humans” by Georgina Gonzalez-Isunza, M. Zaki Jawaid, Pengyu Liu, Daniel L. Cox, Mariel Vazquez, Javier Arsuaga has been accepted for Scientific Reports.

May, 2023 – Anandita De has completed her dissertation and will head to University of Oregon for postdoctoral research! Congratulations Anandita!

April 2023 – Carolyn Chiu and Aspen Drake have undertaken independent studies on protein simulation. Welcome Carolyn and Aspen!

Oct. 2022 – Jiacheng Xu will attend a Janelia Farms workshop on Computational Neuroscience in November – congratulations Jiacheng!

Oct. 2022 – The Cox group will participate in an exciting, funded proposal on “Expedition on Brain-Derived Neuromorphic Computing with Intelligent Photonic and Electronic Materials,” led by Prof. Ben Yoo from the Department of Electrical and Computer Engineering from UC Davis.

Aug 2022 – Prof. Cox has retired from his Distinguished Professor Position at UC Davis, but as Distinguished Professor Emeritus will still oversee graduate and undergraduate research, and he will continue to serve as Chief Operations Officer for Protein Architects Corporation.

June/July 2022 – Zaki Jawaid has graduated from UC Davis with his PhD in Physics, and started work as a Data Scientist at EpicBio in South San Francisco. Congratulations Zaki!

Jan. 2022 – “Computational study of the furin cleavage domain of SARS-CoV-2: delta binds strongest of extant variants” by M.Z. Jawaid et al. posted to bioRxiv.

Dec. 2021 – “Simulation of the omicron variant of SARS-CoV-2 shows broad antibody escape, weakened ACE2 binding, and modest increase in furin binding” by M.Z. Jawaid et al. posted to bioRxiv.

Nov. 2021 – “Neurodegenerative damage reduces firing coherence in a continuous attractor model of grid cells,” by Dr. Y . Zhi and D.L. Cox published in Physical Review E.

Nov. 2021 – “A biophysical model for plant cell plate maturation based upon the contribution of a spreading force,” by M.Z. Jawaid et al. published in Plant Physiology.

Aug. 2021 – Congratulations to Dr. Yuduo Zhi, PhD! Yuduo next begins work at Tencent Company

Aug. 2021 – Congratulations to Kendall Berry! Increased oscillatory power in a computational model of the olfactory bulb due to synaptic degeneration is published in Physical Review E.

June 2021 – Congratulations to Rustin Mahboubi-Ardakani and Joseph McTiernan for completion of Seniors Honors Theses with Highest Honors in Physics at UC Davis. Joseph begins graduate study in physics at UC Merced in August 2021, and Rustin is applying to medical school for next year.

Sept. 2020 – Congratulations to Dr. Rachel Baarda, PhD! Rachel is now working at IDbyDNA

Aug. 2020. Neurodegenerative damage reduces firing coherence in a continuous attractor model of grid cells, by Yuduo Zhi and Daniel Cox, submitted to Physical Review E.

Aug. 2020. Paper on modeling the auditory processing system necessary for localization of sounds in the vertical direction by Anandita De and Daniel Cox posted to BioRXiv.

Aug. 2020. Paper on modeling the effect of neurodegenerative damage on the processing of odors in the olfactory bulb by Kendall Berry and Daniel Cox posted to BioRXiv. UPDATE: Published in Physical Review E Aug. 2021

June 2020: Collaboration with Prof. Michael Toney on designing proteins to help capture the Sars-COV-2 virus discussed here, here, and here.

May 2020: Our first plant biology paper, A Biophysical Model for Plant Cell Plate Development, led by Zaki Jawaid in collaboration with Prof. Georgia Drakakaki and Rosalie Sinclair, has been submitted to Biophysical Journal and posted on biorxiv.

Winter 2020; Congratulations to Jiacheng Xu for completing his general/admission to candidacy exam!

January 2020: Congratulations to Jiacheng Xu for participating in the prestigious IBRO-Simons Summer School on Neuroscience

Summer 2020: Congratulations to Yuduo Zhi and Muhammad Zaki Jawaid for passing their general/admission to candidacy exams!

Spring 2020: Congratulations to Kendall Berry and Anandita De for passing their general/admission to candidacy exams!

9/20/18 – Rachel Baarda, Tegan Mariunchuk, Michael Toney, and Daniel Cox have just gotten the paper “In silico Stress-Strain Measurements on Self-assembled Protein Lattices” published online in Soft Matter. Rachel Baarda prepared a figure that will be the cover art for the print edition of the journal!

News: 7/1/2018 – Dr. Cox is co-PI of US NSF MCB-1818219 “Dissecting molecular mechanisms of plant cytokinesis and cell plate development”, lead PI Prof. Georgia Drakakaki of UC Davis Plant Science. The work will focus on developing theoretical models of cell plate formation during plant cytokinesis.

News: 6/15/18 – Amanda Parker receives her PhD from UC Davis – dissertation title is: Molecular Dynamics Studies of the Mechanical Properties and
Self-Assembly of Beta-Solenoid Proteins– Dr Parker is now a postdoctoral researcher at Syracuse University in the Department of Physics

News: 8/10/17 – Amanda Parker, Krishna Ravikumar, and Daniel L Cox have just gotten the paper “Molecular Dynamics-Based Strength Estimates of Beta-Solenoid Proteins” accepted in Soft Matter

8/9/17 Aaron Chan, who has volunteered in the group for 2+ years, is off to graduate study in biophysics at the University of Illinois, Urbana-Champaign!

6/17-7/17 – Rachel Baarda and Amanda Parker have participated in the Cargese Summer School on Theoretical Biophysics!