Quantifying the Dynamics of Protein Self-Organization Using Deep Learning Analysis of Atomic Force Microscopy Data
Maxim Ziatdinov, Shuai Zhang, Orion Dollar, Jim Pfaendtner, Christopher J. Mundy, Xin Li, Harley Pyles, David Baker, James J. De Yoreo, and Sergei V. Kalinin.

Nano Letters (In Press)

DOI: 10.1021/acs.nanolett.0c03447

December 11, 2020

Programming Amphiphilic Peptoid Oligomers for Hiearchical Assembly and Inorganic Crystallization
Bin Cai, Zhiliang Li, and Chun-Long Chen

Accounts of Chemical Research (In Press)

DOI: 10.1021/acs.accounts.0c00533

November 2, 2020

Orientation and Conformation of Proteins at the Air-Water Interface Determined from Integrative Molecular Dynamics Simulations and Sum Frequency Generation Spectroscopy

Sarah Alamdari, Steven J. Roeters, Thaddeus W. Golbek, Lars Schmüser, Tobias Weidner, and Jim Pfaendtner

Langmuir (Volume 36, Issue 40,  Pages 11855-11865)

DOI: 10.1021/acs.langmuir.0c01881

September 12, 2020

Closing the Gap Between Modeling and Experiments in the Self-Assembly of Biomolecules at Interfaces and in Solution 

Janani Sampath, Sarah Alamdari, and Jim Pfaendtner

Chemistry of Materials (Volume 32, Issue 19,  Pages 8043-8059)

DOI: 10.1021/acs.chemmater.0c01891

August 17, 2020

MARTINI-Compatible Coarse-Grained Model for the Mesoscale Simulation of Peptoids

Mingfei Zhao, Janani Sampath, Sarah Alamdari, Gillian Shen, Chun-Long Chen, Christopher J. Mundy, Jim Pfaendtner, and Andrew L. Ferguson

The Journal of Physical Chemistry B (Volume 124, Issue 36,  Pages 7745-7764)

DOI: 10.1021/acs.jpcb.0c04567

August 10, 2020

Peptoid-Based Programmable 2D Nanomaterial Sensor for Selective and Sensitive Detection of H2S in Live Cells

Mingming Wang, Yang Song, Peng Mu, Xiaoli Cai, Yuehe Lin, and Chun-Long Chen

ACS Applied Bio Materials (Volume 3, Issue 9,  Pages 6039-6048)

DOI: 10.1021/acsabm.0c00657

August 9, 2020

Covalently Lined, Two-Dimensional Quantum Dot Assemblies
Andrew Ritchhart, Madison Monahan, Julian Mars, Michael F. Toney, James J. De Yoreo, and Brandi M. Cossairt

Langmuir (Volume 36, Issue 33,  Pages 9944-9951)

DOI: 10.1021/acs.langmuir.0c01668

July 29, 2020

Assembly of a Patchy Protein into Variable 2D Lattices via Tunable Multiscale Interactions

Shuai Zhang, Robert G. Alberstein, James J. De Yoreo, and F. Akif Tezcan

Nature Communications (Volume 11,  Pages 1-12)

DOI: 10.1038/s41467-020-17562-1

July 28, 2020

Engineering Biomolecular Self-Assembly at Solid-Liquid Interfaces

Shuai Zhang, Jiajun Chen, Jianli Liu, Harley Pyles, David Baker, Chun-Long Chen, and James J. De Yoreo 

Advanced Materials (Online Only)

DOI: 10.1002/adma.201905784

July 6, 2020

Phase Control of Nanocrystalline Inclusions in Bioprecipated Titania with a Panel of Mutant Silica-Binding Proteins

Brittney Hellner, Amy E. Stegmann, Karthik Pushpavanam, Matthew J. Bailey, and François Baneyx

Langmuir (Volume 36, Issue 29, Pages 8503-8510)

DOI: 10.1021/acs.langmuir.0c01108

July 2, 2020

Peptoid-Based Hierarchically-Structured Biomimetic Nanomaterials: Synthesis, Characterization and Applications
Jianli Liu, Bin Cai, Lifeng Cui, and Chun-Long Chen

Science China Materials (Volume 63, Issue 7, Pages 1099-1112)

DOI: 10.1007/s40843-020-1296-8

April 22, 2020

Molecular Recognition and Specificity of Biomolecules to Titanium Dioxide from Molecular Dynamics Simulations

Janani Sampath, Andrew Kullman, Rachel Gebhart, Gary Drobny, and Jim Pfaendtner

npj Computational Materials (Volume 6, Pages 1-8)

DOI: 10.1038/s41524-020-0288-7

April 7, 2020

Estimating Presiach Density via Subset Selection

Xin Li, Dohyung Kim, Sabine M. Neumayer, Mahshid Ahmadi, and Sergei Kalinin

IEEE Access (Volume 8, Pages 61767-61774)

DOI: 10.1109/ACCESS.2020.2983364

March 20, 2020

Sequence-Structure-Binding Relationships Reveal Adhesion Behavior of the Car9 Solid-Binding Peptide: An Integrated Experimental and Simulation Study

Brittney Hellner, Sarah Alamdari, Harley Pyles, Shuai Zhang, Arushi Prakash, Kayla G. Sprenger, James J. De Yoreo, David Baker, Jim Pfaendtner, and François Baneyx

Journal of the American Chemical Society (Volume 142, Issue 5, Pages 2355-2363)

DOI: 10.1021/jacs.9b11617

January 14, 2020

Bioinspired Peptoid Nanotubes for Targeted Tumor Cell Imaging and Chemo-Photodynamic Therapy

Yanan Luo, Yang Song, Mingming Wang, Tengyue Jian, Shichao Ding, Peng Mu, Zhihao Liao, Qiurong Shi, Xiaoli Cai, Haibao Jin, Dan Du, Wen-Ji Dong, Chun-Long Chen, and Yuehe Lin

Small (Volume 15, Issue 43, Pages 1-8)

DOI: 10.1002/smll.201902485

August 30, 2019

Amphiphilic Peptide Binding on Crystalline vs. Amorphous Silica from Molecular Dynamics Simulations

Janani Sampath and Jim Pfaendtner

Molecular Physics (Volume 117, Issue 23-24, Pages 3642-3650)

DOI: 10.1080/00268976.2019.1657192

August 25, 2019

Controlling Protein Assembly on Inorganic Crystals Through Designed Protein Interfaces

Harley Pyles, Shuai Zhang, James J. De Yoreo, and David Baker

Nature (Volume 571, Issue 7764, Pages 251-256)

DOI: 10.1038/s41586-019-1361-6

July 10, 2019

Modeling the Cooperative Adsorption of Solid-Binding Proteins on Silica: Molecular Insights from Surface Plasmon Resonance Measurements

Brittney Hellner, Seong Beom Lee, Akshay Subramaniam, Venkat R. Subramanian, and François Baneyx

Langmuir (Volume 35, Issue 14, Pages 5013-5020)

DOI: 10.1021/acs.langmuir.9b00283

March 14, 2019

Selective Labeling and Decoration of the Ends and Sidewalls of Single-Walled Carbon Nanotubes Using Mono- and Bispecific Solid-Binding Fluorescent Proteins

Sonja J.G. Dunakey, Brandon L. Coyle, Alexander Thomas, Meng Xu, Brian J.F. Swift, and François Baneyx

Bioconjugate Chemistry (Volume 30, Issue 3, Pages 959-965)

DOI: 10.1021/acs.bioconjchem.9b00097

February 28, 2019

 

PUBLICATIONS

SUBMITTED PAPERS

The following papers have been submitted for publication in peer-reviewed journals.

Peptoid-Directed Assembly of CdSe Nanoparticles
M. Monahan, B. Cai, T. Jian, S. Zhang, G. Zhu, C-L Chen, J.J. De Yoreo, and B. Cossairt

Solid-Binding Proteins: Bridging Synthesis and Function in Hybrid and Hierarchical Materials Fabrication

K. Pushpavanam, J. Ma, Y. Cai, N.Y. Naser, and F. Baneyx

Decoding Biomineralization One Amino Acid at a Time: Influence of Silica-Binding Proteins on the Morphology of Bioprecipitated Titania in a Diffusion-Controlled Setup

K. Pushpavanam, B. Hellner, and F. Baneyx

Rational Design of Protein-Peptoid Hybrid Nanosheets for the Construction of Hierarchical Nanostructure

J. Ma, B.  Cai, S. Zhang, T. Jian, J.J. De Yoreo, C-L Chen, and F. Baneyx

Rotational States and Transition Mechanisms of Surface-Adsorbed Proteins

S. Zhang, R. Sadre, B.A. Legg, H. Pyles, T. Perciano, E.W. Bethel, D. Baker, O. Rübel, and J.J. De Yoreo

Strong Coupling Between Silver Nanoparticles and Hybrid Photon-Exciton Fano Resonances in Two-Dimensional Organic-Inorganic Perovskite Thin Films

F. Muckel, K.N. Guye, S.M. Gallagher, Y. Liu, and D.S. Ginger

Exploring Particle Dynamics During Self-Organization Processes via Rotationally Invariant Latent Representations

S.V. Kalinin, S. Zhang, M. Valleti, H. Pyles, D. Baker, J.J. De Yoreo, and M. Ziatdinov

©2020 Center for the Science of Synthesis Across Scales