M. Cheung

发表

Relative Cosolute Size Influences the Kinetics of Protein-Protein Interactions.

M. Waxham, J. Putkey, Xu Wang, 2015, Biophysical journal.

Domain swapping is a consequence of minimal frustration.

Samuel S. Cho, J. Onuchic, P. Wolynes, 2004, Proceedings of the National Academy of Sciences of the United States of America.

The energy landscape for protein folding and possible connections to function

Margaret S. Cheung, José N. Onuchic, Leslie L. Chavez, 2004 .

Protein folding mediated by solvation: Water expulsion and formation of the hydrophobic core occur after the structural collapse

J. Onuchic, A. Garcia, M. Cheung, 2002, Proceedings of the National Academy of Sciences of the United States of America.

Mechanisms of cooperativity underlying sequence-independent β-sheet formation

Margaret S. Cheung, Herbert Levine, David A. Kessler, 2001, cond-mat/0104065.

Computational studies of the reversible domain swapping of p13suc1.

Jorge Chahine, M. Cheung, J. Chahine, 2005, Biophysical journal.

Macromolecular crowding modulates folding mechanism of alpha/beta protein apoflavodoxin.

Dirar Homouz, Pernilla Wittung-Stafshede, P. Wittung-Stafshede, 2008, Biophysical journal.

Molecular crowding enhances native structure and stability of α/β protein flavodoxin

P. Wittung-Stafshede, M. Cheung, Loren J. Stagg, 2007, Proceedings of the National Academy of Sciences.

Solvation in protein folding analysis: combination of theoretical and experimental approaches.

M Wilmanns, L Serrano, J. Onuchic, 2004, Proceedings of the National Academy of Sciences of the United States of America.

Molecular crowding enhances native state stability and refolding rates of globular proteins.

D. Thirumalai, D. Klimov, M. Cheung, 2005, Proceedings of the National Academy of Sciences of the United States of America.

The Role of Protein Dynamics in Calmodulin Target Recognition

M. Waxham, J. Putkey, Xu Wang, 2014 .

A physics-based approach of coarse-graining the cytoplasm of Escherichia coli (CGCYTO).

Qian Wang, Q. Wang, M. Cheung, 2012, Biophysical journal.

Multiscale simulation on a light-harvesting molecular triad.

M. Cheung, D. Homouz, G. Su, 2012, The journal of physical chemistry. B.

Lessons in Protein Design from Combined Evolution and Conformational Dynamics

Margaret S. Cheung, M. Neal Waxham, Swarnendu Tripathi, 2015, Scientific Reports.

Conformational frustration in calmodulin–target recognition

M. Waxham, Swarnendu Tripathi, Laurel Hoffman, 2015, Journal of molecular recognition : JMR.

Multiscale investigation of chemical interference in proteins.

Dirar Homouz, Antonios Samiotakis, M. Cheung, 2010, The Journal of chemical physics.

Molecular-Level Exploration of the Structure-Function Relations Underlying Interfacial Charge Transfer in the Subphthalocyanine/ C60 Organic Photovoltaic System

B. Dunietz, M. Cheung, Eitan Geva, 2020 .

Molecular Dynamics Ensemble Refinement of Intrinsically Disordered Peptides According to Deconvoluted Spectra from Circular Dichroism

M. Waxham, M. Cheung, Pengzhi Zhang, 2020, Biophysical journal.

Competition of individual domain folding with inter-domain interaction in WW domain engineered repeat proteins.

M. Gruebele, M. Cheung, Kapil Dave, 2019, Physical chemistry chemical physics : PCCP.

Correction to "Theoretical Investigations of the Role of Mutations in Dynamics of Kinesin Motor Proteins".

A. Kolomeisky, Qian Wang, M. Cheung, 2018, The journal of physical chemistry. B.

CTRAMER: An open-source software package for correlating interfacial charge transfer rate constants with donor/acceptor geometries in organic photovoltaic materials.

B. Dunietz, M. Cheung, Eitan Geva, 2021, The Journal of chemical physics.

Effects of macromolecular crowding agents on protein folding in vitro and in silico

Alexander F. Christiansen, Q. Wang, P. Wittung-Stafshede, 2013, Biophysical Reviews.

Where soft matter meets living matter--protein structure, stability, and folding in the cell.

M. Cheung, 2013, Current opinion in structural biology.

Classification : Biological Sciences Molecular Origin of the Weak Susceptibility of Kinesin Velocity to Loads and its Relation to the Collective Behavior of Kinesins Short title : Molecular Origin of the Weak Susceptibility of Kinesin

J. Onuchic, A. Kolomeisky, Q. Wang, 2017 .

A Physics-based Approach of Coarse-graining the cytoplasm of E. coli

Q. Wang, M. Cheung, 2012 .

Opposing Intermolecular Tuning of Ca2+ Affinity for Calmodulin by Neurogranin and CaMKII Peptides

Swarnendu Tripathi, M. Cheung, Pengzhi Zhang, 2017, Biophysical journal.

Folding dynamics of Trp-cage in the presence of chemical interference and macromolecular crowding. I.

M. Cheung, Antonios Samiotakis, 2011, The Journal of chemical physics.

Manipulating biopolymer dynamics by anisotropic nanoconfinement.

M. Cheung, Shao-Qing Zhang, 2007, Nano letters.

Photoinduced Charge Transfer Dynamics in the Carotenoid-Porphyrin-C60 Triad via the Linearized Semiclassical Nonequilibrium Fermi's Golden Rule.

B. Dunietz, M. Cheung, Zhubin Hu, 2020, The journal of physical chemistry. B.

Effects of Protein Crowders and Charge on the Folding of Superoxide Dismutase 1 Variants: A Computational Study.

M. Cheung, G. Morrison, Atrayee Sarkar, 2022, The journal of physical chemistry. B.

Graph identification of proteins in tomograms (GRIP‐Tomo)

James A. Evans, Doo Nam Kim, Trevor H. Moser, 2022, Protein science : a publication of the Protein Society.

A generalized Flory-Stockmayer kinetic theory of connectivity percolation and rigidity percolation of cytoskeletal networks

Nicholas P. Schafer, P. Wolynes, N. Schafer, 2022, PLoS Comput. Biol..

Multiscale simulation of the ground and photo-induced charge-separated states of a molecular triad in polar organic solvent: exploring the conformations, fluctuations, and free energy landscapes.

H. Lischka, A. Aquino, D. Balamurugan, 2013, The journal of physical chemistry. B.

The role of the Arp2/3 complex in shaping the dynamics and structures of branched actomyosin networks

Nicholas P. Schafer, M. Waxham, P. Wolynes, 2020, Proceedings of the National Academy of Sciences.

Determining the atomic charge of calcium ion in a calcium-binding protein requires the information of its dynamic coordination geometry in aqueous solution

P. Cieplak, M. Cheung, Jaebeom Han, 2020, 2011.07639.

Assemblies of calcium/calmodulin-dependent kinase II with actin and their dynamic regulation by calmodulin in dendritic spines

Nicholas P. Schafer, M. Waxham, P. Wolynes, 2019, Proceedings of the National Academy of Sciences.

Protein recognition and selection through conformational and mutually induced fit

M Neal Waxham, Dirar Homouz, Qian Wang, 2013, Proceedings of the National Academy of Sciences.

Insights from graph theory on the morphologies of actomyosin networks with multilinkers.

H. Levine, F. Nédélec, M. Cheung, 2020, Physical review. E.

Multivalent actin-binding proteins augment the variety of morphologies in actomyosin networks

H. Levine, F. Nédélec, M. Cheung, 2020, 2006.06503.

Folding, Stability and Shape of Proteins in Crowded Environments: Experimental and Computational Approaches

Margaret S. Cheung, Pernilla Wittung-Stafshede, Antonios Samiotakis, 2009, International journal of molecular sciences.

Induced polarization restricts the conformational distribution of a light-harvesting molecular triad in the ground state.

P. Cieplak, M. Cheung, Pengzhi Zhang, 2017, Physical chemistry chemical physics : PCCP.

Correlation between Gene Variants, Signaling Pathways, and Efficacy of Chemotherapy Drugs against Colon Cancers

Swarnendu Tripathi, R. Bose, M. Cheung, 2016, Cancer informatics.

Crowded, cell-like environment induces shape changes in aspherical protein

Dirar Homouz, Pernilla Wittung-Stafshede, Antonios Samiotakis, 2008, Proceedings of the National Academy of Sciences.

Molecular mechanisms of the interhead coordination by interhead tension in cytoplasmic dyneins

J. Onuchic, A. Kolomeisky, M. Diehl, 2018, Proceedings of the National Academy of Sciences.

Understanding protein-complex assembly through grand canonical maximum entropy modeling

M. Cheung, A. Sarkar, Andrei G. Gasic, 2021, Physical Review Research.

Structure, function, and folding of phosphoglycerate kinase are strongly perturbed by macromolecular crowding

Dirar Homouz, Martin Gruebele, Antonios Samiotakis, 2010, Proceedings of the National Academy of Sciences.

Effects of macromolecular crowding on burst phase kinetics of cytochrome c folding.

Alexander F. Christiansen, P. Wittung-Stafshede, D. Kliger, 2012, Biochemistry.

CATS: A Tool for Clustering the Ensemble of Intrinsically Disordered Peptides on a Flat Energy Landscape.

M. Cheung, Jacob C Ezerski, 2018, The journal of physical chemistry. B.

The Effect of Macromolecular Crowding, Ionic Strength and Calcium Binding on Calmodulin Dynamics

Margaret S. Cheung, Qian Wang, M. Neal Waxham, 2011, PLoS Comput. Biol..

Modulation of calmodulin plasticity by the effect of macromolecular crowding.

M Neal Waxham, Dirar Homouz, Hugo Sanabria, 2009, Journal of molecular biology.

Pathways of electron transfer in Escherichia coli DNA photolyase: Trp306 to FADH.

A. Stuchebrukhov, M. Cheung, I. Daizadeh, 1999, Biophysical journal.

Factors defining effects of macromolecular crowding on protein stability: an in vitro/in silico case study using cytochrome c.

Qian Wang, Alexander F. Christiansen, Pernilla Wittung-Stafshede, 2010, Biochemistry.

Potential quantum advantage for simulation of fluid dynamics

Xiaolong Yin, N. Wiebe, G. Schenter, 2023, 2303.16550.

Nanopore-protein interactions dramatically alter stability and yield of the native state in restricted spaces.

D. Thirumalai, M. Cheung, 2006, Journal of molecular biology.

BRCA1 and BRCA2 mutations sensitize to chemotherapy in patient-derived pancreatic cancer xenografts

R. Bristow, Alexander Borgida, M. Tsao, 2015, British Journal of Cancer.

Towards developing principles of protein folding and dynamics in the cell

M. Cheung, Andrei G. Gasic, 2018, Physical biology.

Influence of the shape of crowding particles on the structural transitions in a polymer.

D Thirumalai, D. Thirumalai, A. Kudlay, 2012, The journal of physical chemistry. B.

Residue-specific analysis of frustration in the folding landscape of repeat beta/alpha protein apoflavodoxin.

P. Wittung-Stafshede, M. Cheung, D. Homouz, 2010, Journal of molecular biology.

Fundamental Gaps of Condensed-Phase Organic Semiconductors from Single-Molecule Calculations using Polarization-Consistent Optimally Tuned Screened Range-Separated Hybrid Functionals.

L. Kronik, B. Dunietz, M. Cheung, 2018, Journal of chemical theory and computation.

Effects of macromolecular crowding agents on protein folding in vitro and in silico

Alexander F. Christiansen, P. Wittung-Stafshede, M. Cheung, 2013, Biophysical Reviews.

Impact of hydrodynamic interactions on protein folding rates depends on temperature.

M. Cheung, D. Homouz, Yossi Eliaz, 2017, Physical review. E.

On the Interplay between Electronic Structure and Polarizable Force Fields When Calculating Solution-Phase Charge-Transfer Rates.

B. Dunietz, M. Cheung, Jaebeom Han, 2020, Journal of chemical theory and computation.

Unraveling the Mechanism of Photoinduced Charge Transfer in Carotenoid-Porphyrin-C60 Molecular Triad.

D. Balamurugan, B. Dunietz, A. Manna, 2015, The journal of physical chemistry letters.

Critical phenomena in the temperature-pressure-crowding phase diagram of a protein.

Maxim B. Prigozhin, M. Gruebele, M. Cheung, 2019, Physical review. X.

A Robust Communication Framework for Parallel Execution on Volunteer PC Grids

David P. Anderson, Jaspal Subhlok, Qian Wang, 2011, 2011 11th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing.

REDUNDANCY TOLERANT COMMUNICATION ON VOLATILE NODES

Jaspal Subhlok, Edgar Gabriel, Nagarajan Kanna, 2008 .

Charge transfer rate constants for the carotenoid-porphyrin-C60 molecular triad dissolved in tetrahydrofuran: The spin-boson model vs the linearized semiclassical approximation.

B. Dunietz, M. Cheung, Eitan Geva, 2020, The Journal of chemical physics.

Electrostatics, structure prediction, and the energy landscapes for protein folding and binding

Peter G Wolynes, Nicholas P Schafer, Weihua Zheng, 2016, Protein science : a publication of the Protein Society.

Crowding-Induced Elongated Conformation of Urea-Unfolded Apoazurin: Investigating the Role of Crowder Shape in Silico.

P. Wittung-Stafshede, M. Cheung, D. Homouz, 2019, The journal of physical chemistry. B.

Biophysical properties of membrane-active peptides based on micelle modeling: a case study of cell-penetrating and antimicrobial peptides.

G. Hong, M. Cheung, R. Pachter, 2010, The journal of physical chemistry. B.

Forecasting Avalanches in Branched Actomyosin Networks with Network Science and Machine Learning.

M. Cheung, Yossi Eliaz, Chengxuan Li, 2021, The journal of physical chemistry. B.

Exploring the Interplay between Topology and Secondary Structural Formation in the Protein Folding Problem

Margaret S. Cheung, José N. Onuchic, J. Onuchic, 2003 .

Manipulating biopolymer dynamics by anisotropic nanoconfinement.

M. Cheung, Shao-Qing Zhang, 2007, Nano letters.

A structural model of polyglutamine determined from a host-guest method combining experiments and landscape theory.

José N Onuchic, J. Onuchic, M. Cheung, 2004, Biophysical journal.

Hydrophobic interactions of hexane in nanosized water droplets.

M. Cheung, D. Homouz, B. Hoffman, 2009, The journal of physical chemistry. B.

Correlating Interfacial Charge Transfer Rates with Interfacial Molecular Structure in the Tetraphenyldibenzoperiflanthene/C70 Organic Photovoltaic System.

B. Dunietz, M. Cheung, Eitan Geva, 2022, The journal of physical chemistry letters.

The Zero-Order Loop in Apoazurin Modulates Folding Mechanism In Silico.

P. Wittung-Stafshede, M. Cheung, D. Homouz, 2021, The journal of physical chemistry. B.

Comparison of chemical and thermal protein denaturation by combination of computational and experimental approaches. II.

Alexander F. Christiansen, P. Wittung-Stafshede, M. Cheung, 2011, The Journal of chemical physics.

Cysteine-cysteine contact preference leads to target-focusing in protein folding.

Mihaela E. Sardiu, Yi-Kuo Yu, M. Cheung, 2007, Biophysical journal.

Crowding effects on the structural transitions in a flexible helical homopolymer.

D. Thirumalai, A. Kudlay, M. Cheung, 2009, Physical review letters.

Effects of crowding and confinement on the structures of the transition state ensemble in proteins.

D Thirumalai, D. Thirumalai, M. Cheung, 2007, The journal of physical chemistry. B.

pointerchain: Tracing pointers to their roots - A case study in molecular dynamics simulations

Millad Ghane, Sunita Chandrasekaran, Margaret S. Cheung, 2019, Parallel Comput..

Molecular origin of the weak susceptibility of kinesin velocity to loads and its relation to the collective behavior of kinesins

Margaret S. Cheung, Anatoly B. Kolomeisky, Michael R. Diehl, 2017, Proceedings of the National Academy of Sciences.

Calmodulin, Models of

Margaret S. Cheung, M. Neal Waxham, M. Waxham, 2014, Encyclopedia of Computational Neuroscience.

A Tale of Two Desolvation Potentials: An Investigation of Protein Behavior under High Hydrostatic Pressure.

M. Cheung, Andrei G. Gasic, 2019, The journal of physical chemistry. B.

Coarse-Grained Modeling and Molecular Dynamics Simulations of Ca2+-Calmodulin

P. Wolynes, M. Cheung, Kaitlin Knapp, 2021, Frontiers in Molecular Biosciences.

Folding Dynamics of Trp-Cage in the Presence of Chemical Interference and Macromolecular Crowding

M. Cheung, Antonios Samiotakis, 2012 .

Experiment and Simulation Reveal Residue Details for How Target Binding Tunes Calmodulin's Calcium-Binding Properties.

M. Waxham, M. Cheung, Pengzhi Zhang, 2023, The journal of physical chemistry. B.