Publications ('*' indicates corresponding author[s])
An exhaustive survey of regular peptide conformations using a new metric for backbone handedness (h).
PeerJ (2017) 5:e3327
Structure based sequence analysis of viral and cellular protein assemblies.
Journal of Structural Biology (2016) in press
The Ramachandran number: an order parameter for protein geometry.
PLoS ONE (2016) 11(8):e0160023
Predicting the outcome of the growth of binary solids far from equilibrium.
Physical Review E (2016) 93:042136
Design, Synthesis, and Assembly of Peptoid Nanosheets.
Accounts of Chemical Research (2016) 49:(3)379
Journal cover [link];
Most downloaded paper in January [link].
Landscape of kinetically trapped binary assemblies.
Journal of Chemical Physics (2015) 143:214902
Peptoid nanosheets exhibit a new secondary structure motif.
Nature (2015) 526:415
Featured by C&E News [link], Berkeley Lab [link] and 8 other news sites [link].
Two-component metal-organic framework displaying compositional robustness to solution constitution.
Proceedings of the National Academy of Sciences (2015) 112(18):5591
*: Equal contribution.
Featured in a Phys.org article [link].
Modeling sequence-specific polymers using anisotropic coarse-grained sites allows quantitative comparison with experiment.
Journal of Chemical Theory and Computation (2015) 11(1):303
Growth of equilibrium structures built from a large number of distinct component types.
Soft Matter (2014) 10(34):6404
Journal cover [link]; Featured as a “hot paper” of 2014 [link].
Origination of the protein fold repertoire from oily pluripotent peptides.
Proteomes (2014) 2(2):154
Dynamic new world: refining our view of protein structure, function and evolution.
Proteomes (2014) 2(1):128
Figure reused in textbook Introduction to Protein Science (3rd Ed), Arthur Lesk (Author), Oxford University Press.
Development and use of an atomistic CHARMM-based forcefield for peptoid simulation.
Journal of Computational Chemistry (2014) 35(5):360
Journal cover [link]; Featured by the Department of Defense [link]; Mentioned as “important upcoming paper” [link].
Two modes of protein sequence evolution and their compositional dependencies.
Physical Review E (2013) 87(6):062714
A universal trend among proteomes indicates an oily last common ancestor.
PLoS Computational Biology (2012) 8(12):e1002839
In the news as a GenomeWeb.com paper of note, 01/25/2013. [link]
Multiscale modeling of virus structure, assembly and dynamics.
Chapter in Book: Computational Modeling of Biological Systems: From Molecules to Pathways. (2011) Springer Berlin. ISBN 9781461421450. Ed: Dokholyan, N
[link|please inquire for pdf].
Periodic table of virus capsids: implications for natural selection and design.
PLoS ONE (2010) 5(3):e9423
Discussed in textbooks:Principles of Molecular Virology, Alan Cann (Author), Academic Press; Nanomedicine (Frontiers of Nanoscience), Huw D Summers (Editor), Elsevier.
Discussed in book for utility of math in biology: The Emergence and Nature of Human History Volume One, Joseph Miller.
Principles of virus capsid design.
ProQuest Publishing (2010) ISBN # 9781109683769
Geometric considerations in capsid size-specificity, auxiliary requirements and buckling.
Proceedings of the National Academy of Sciences (2009) 106(21):8531
Tilable nature of virus capsids and the role of topological constraints in natural capsid design.
Physical Review E (2008) 77(5):051902
Feature story by the American Physical Society for advancing structural virology in the article “Piecing a Virus Together”, Phys. Rev. Focus, 21:18. [link]
P-PIDA: a long-range pattern detection algorithm for proteins.
University of Houston Library (2004) Senior Honors Thesis.
Winner of the University of Houston Outstanding Senior Thesis Award.