Biological Physics Publications from the group

In silico stress–strain measurements on self-assembled protein lattices, Rachel A. Baarda, Tegan Marianchuk, Michael Toney, and Daniel L. Cox, Soft Matter (2018).

“High Tensile Strength of Engineered β-Solenoid Fibrils via Sonication and Simulations” Z. Peng, A.S. Parker, M.D.R. Peralta, K.M. Ravikumar, D.L. Cox, and M.D. Toney, Biophysical Journal 113, 1945-1955 (2017).

“Molecular Dynamics-Based Strength Estimates of Beta-Solenoid Proteins”, Amanda S. Parker, Krishnakumar Ravikumar, and Daniel L. Cox, accepted for publication in Soft Matter, Aug. 2017. Also posted on arxiv here

A Model for Competing Pathways in protein-aggregation: role of membrane bound proteins,”
Youval Dar, Daniel Cox, Rajiv Singh, submitted to Phys. Rev. E (2016) posted at

Local Mechanical Perturbation Provides an Effective Means to Regulate the Growth and Assembly of Functional Peptide Fibrils,”  Arpad Karsai, Teri Jo Slack, Hamed Malekan, Fadi Khoury, Wei‐Feng Lin, Victoria Tran, Daniel Cox, Michael Toney, Xi Chen, Gang‐yu Liu, Small, 10.1002/smll.201601657 (2016)

In silico measurements of twist and bend moduli
for beta solenoid protein self-assembly units,” Leonard Heinz, Krishnakumar M. Ravikumar, and Daniel L. Cox, accepted for publication in Nano Letters (4/27/15).

Structures of Bacteroides fragilis uridine 5′-diphosphate-N-acetylglucosamine (UDP-GlcNAc) acyltransferase (BfLpxA),”
A. Ngo, K. T. Fong, D. L. Cox, X. Chen and A. J. Fisher, Acta Cryst. (2015). D71, doi:10.1107/S1399004715003326

‘Engineering Amyloid Fibrils from β-solenoid Proteins for Biomaterials Applications’, Maria D.R. Peralta, Arpad Karsai, Alice Ngo, Catherine Sierra, Kai T. Fong, Natha Robert Hayre, Nima Mirzaee, Krishnakumar Mayuram Ravikumar, Alexander J. Kluber, Xi Chen, Gang-yu Liu, Michael D. Toney, Rajiv. R. Singh, and Daniel Lee Cox, accepted for ACS Nano, Jan. 2015. (

“Simulated Cytoskeletal Collapse Via Tau Degradation,” A. Sendek, H.R. Fuller, N.R. Hayre, R.R.P. Singh, and D.L. Cox, PLoS ONE 9(8): e104965. doi:10.1371/journal.pone.0104965.

“Application of the G-JF discrete-time thermostat for fast and accurate molecular simulations”, Gronbech-Jensen, N. , N.R. Hayre, and O. Farago, Computer Physics Comm. 185:524-527 (2014).

Singh, Jesse P., Paul C. Whitford, N.R. Hayre, José Onuchic, and Daniel
L. Cox. Massive Conformation Change in the Prion Protein: Using
Dual-Basin Structure-Based Models to Find Misfolding Pathways.
Proteins: Structure, Function, Bioinformatics, 80: 1299-1307 (2012)

Hayre, Natha R., Rajiv R.P. Singh, and Daniel L. Cox. Sequence-
Dependent Stability Test of a Left-Handed β-Helix Motif. Biophysical
Journal, 102: 1443-1452.(2012)

Hayre, N.R., R.R.P. Singh, and D.L. Cox. Evaluating Force Field
Accuracy with Long-Time Simulations of a ß-Hairpin Tryptophan
Zipper Peptide. The Journal of Chemical Physics, 134: 035103.
View this Article (2011)

Kunes, Kay C., Scott C. Clark, Daniel L. Cox, and Rajiv R.P. Singh. Left
Handed β Helix Models for Mammalian Prion Fibrils. Prion, 2: 81-90. (2008)

Mallajosyula, Sairam S., J. C. Lin, D. L. Cox, S.K. Pati, and R.R.P. Singh.
Sequence Dependent Electron Transport in Wet DNA: Ab initio and
Molecular Dynamics Studies. Physical Review Letters, 101: 176805. (2008)

Lin, Jong-Chin, Rajiv R.P. Singh, and Daniel L. Cox. Theoretical Study
of DNA Damage Recognition via Electron Transfer from the [4Fe-4S]
Complex of MutY. Biophysical Journal, 95(7): 3259-3268. (2008)

Cox, Daniel L., Jianping Pan, and Rajiv R.P. Sing. A Mechanism for
Copper Inhibition of Infectious Prion Conversion. Biophysical Journal:
Biophysical Letters, 91: L11-L13. (2006)

Cox, Daniel L., Rajiv R.P. Singh, and Sichun Yang. Prion Disease:
Exponential Growth Requires Membrane Binding. Biophysical Journal:
Biophysical Letters, 90: L77-L79 (2006)

Kunes, K.C., D.L. Cox, and R.R.P. Singh. One Dimensional Model of
Yeast Prion Aggregation. Physical Review E, 72: 051915 (2005)

Yang, Sichu, Herbert Levine, José N. Onuchic, and Daniel L. Cox.
Structure of Infectious Prions: Stabilization by Domain Swapping.
FASEB Journal, 19: 1778-1782. (2005)

Cox, D.L., H. Lashuel, K.Y. Lee, and R.R.P. Singh. The Materials
Science of Amyloid Disease. MRS Bulletin, 30: 452.(2005)

Endres, R.G., A. Huebsch, D.L. Cox, and R.R.P. Singh. Electronic
Properties of DNA: From Elementary Slater-Koster-Hueckel Theory
of the π-stack to Ab Initio Calculations of the Optical Conductivity.
Modern Methods for Theoretical Physical Chemistry of Biopolymers.(2005)

Hübsch, A., R.G. Endres, D.L. Cox, and R.R.P. Singh. Optical
Conductivity of Wet DNA. Physical Review Letters, 94: 178102. (2005)

LaBute, M.X., R.G. Endres, and D.L. Cox. An Anderson Impurity Model
for Efficient Sampling of Adiabatic Potential Energy Surfaces of
Transition Metal Complexes. Journal of Chemical Physics, 121: 8221. (2004)

Sengupta, Pinaki, Rajiv R.P. Singh, Daniel L. Cox, and Alex Slepoy.
Lateral Organization of Cholesterol Molecules in Lipid-Cholesterol
Assemblies. Physical Review E, 70: 021902. (2004)

Mobley, D.L., D.L. Cox, R.R.P. Singh, M.W. Maddox, and M.L. Longo.
Modeling Amyloid β-Peptide Insertion into Lipid Bilayers. Biophysical
Journal, 86: 3585-3597.(2004)

Endres, R.G., D.L. Cox and R.R.P. Singh. Colloquium: The Quest for
High-Conductance DNA. Reviews of Modern Physics, 76: 195-214.

Mobley, D.L., D.L. Cox, R.R.P. Singh, R.V. Kulkarni, and A. Slepoy.
Simulations of Oligomeric Intermediates in Prion Diseases.
Biophysical Journal, 85: 2213-2223.(2003)

Endres, R.G., M.X. LaBute, and D.L. Cox. Theory of Adiabatic
Hexaamminecobalt-Self-Exchange. The Journal of Chemical Physics,
118: 8706-8714. (2003)

Kulkarni, R.V., A. Slepoy, R.R.P. Singh, D.L. Cox, and F. Pázmandi.
Theoretical Modeling of Prion Disease Incubation. Biophysical
Journal, 85: 707-718. (2003)

Endres, R.G., D.L. Cox, R.R.P. Singh, and S.K. Pati. Mediation of Long
Range Charge Transfer By Kondo Bound States. Physical Review
Letters, 88: 166601.(2002)

LaBute, M.X., R.V. Kulkarni, R.G. Endres, and D.L. Cox. Strong Electron
Correlations in Cobalt Valence Tautomers. Journal of Chemical
Physics, 116: 3681-3689.(2002)

Slepoy, A., R.R.P. Singh, F. Pázmándi, R.V. Kulkarni, and D.L. Cox.
Statistical Mechanics of Prion Diseases. Physical Review Letters, 87:
058101-058105 (2001)

Other important articles by Prof. Cox and collaborators (out of 108 total)

Bickers, N.E., D.L. Cox, and J.W. Wilkins. Self-Consistent Large-N
Expansion for Normal-State Properties of Dilute Magnetic Alloys.
Physical Review, B36: 2036-2079.(1987)

Cox, D.L. Quadrupolar Kondo Effect in Uranium Heavy Electron
Materials? Physical Review Letters, 59: 1240-1243.(1987)

Cox, D.L. and A. Zawadowski. Exotic Kondo Effects in Metals:
Magnetic Ions in a Crystalline Electric Field and Tunnelling Centres.
Advances in Physics, 47: 599-942.(1998) (Also published as a book by Taylor and Francis)

Cox, D.L. and D. Pines. Introduction to Complex Adaptive Matter.
MRS Bulletin, 30: 425.(2005)

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