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Sara Y Cheng
Sara Y Cheng
Verified email at llnl.gov
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Year
Polarizable force fields for biomolecular simulations: Recent advances and applications
Z Jing, C Liu, SY Cheng, R Qi, BD Walker, JP Piquemal, P Ren
338*
Capturing RNA folding free energy with coarse-grained molecular dynamics simulations
DR Bell, SY Cheng, H Salazar, P Ren
Scientific reports 7 (1), 45812, 2017
462017
Synthetic DNA Melting Probe Enables Differentiation of Four Single-Nucleotide Variants by Melting Temperature
S Cheng, J Obliosca, YA Chen, M Llanos, YL Liu, D Imphean, D Bell, ...
Bulletin of the American Physical Society, 2018
39*2018
Coarse-grained MD simulations reveal beta-amyloid fibrils of various sizes bind to interfacial liquid-ordered and liquid-disordered regions in phase separated lipid rafts with …
SY Cheng, Y Cao, M Rouzbehani, KH Cheng
Biophysical chemistry 260, 106355, 2020
292020
Hydration Free Energy from Orthogonal Space Random Walk and Polarizable Force Field
JR Abella, SY Cheng, Q Wang, W Yang, P Ren
Journal of chemical theory and computation 10 (7), 2792-2801, 2014
192014
LNA thymidine monomer enables differentiation of the four single-nucleotide variants by melting temperature
JM Obliosca, SY Cheng, YA Chen, MF Llanos, YL Liu, DM Imphean, ...
Journal of the American Chemical Society 139 (20), 7110-7116, 2017
182017
Configurational entropy of folded proteins and its importance for intrinsically disordered proteins
M Liu, AK Das, J Lincoff, S Sasmal, SY Cheng, RM Vernon, ...
International journal of molecular sciences 22 (7), 3420, 2021
122021
Maximally asymmetric transbilayer distribution of anionic lipids alters the structure and interaction with lipids of an amyloidogenic protein dimer bound to the membrane surface
SY Cheng, G Chou, C Buie, MW Vaughn, C Compton, KH Cheng
Chemistry and physics of lipids 196, 33-51, 2016
122016
Lipid insertion domain unfolding regulates protein orientational transition behavior in a lipid bilayer
KH Cheng, L Qiu, SY Cheng, MW Vaughn
Biophysical chemistry 206, 22-39, 2015
92015
Characterization of 3D Voronoi tessellation nearest neighbor lipid shells provides atomistic lipid disruption profile of protein containing lipid membranes
SY Cheng, HV Duong, C Compton, MW Vaughn, H Nguyen, KH Cheng
Biophysical chemistry 198, 22-35, 2015
72015
Convergence of stochastic-extended Lagrangian molecular dynamics method for polarizable force field simulation
D An, SY Cheng, T Head-Gordon, L Lin, J Lu
Journal of Computational Physics 438, 110338, 2021
52021
Data supporting beta-amyloid dimer structural transitions and protein–lipid interactions on asymmetric lipid bilayer surfaces using MD simulations on experimentally derived NMR …
SY Cheng, G Chou, C Buie, MW Vaughn, C Compton, KH Cheng
Data in brief 7, 658-672, 2016
42016
Data showing the lipid conformations and membrane binding behaviors of beta-amyloid fibrils in phase-separated cholesterol-enriched lipid domains with and without glycolipid …
SY Cheng, Y Cao, M Rouzbehani, KH Cheng
Data in Brief 30, 105496, 2020
12020
Tracking the transition to turbulence in simulations of hydrodynamic instabilities of National Ignition Facility shock-tube experiments
M Burkey, S Cheng, K Raman, S Nagel, D Bradley, T Ebert, A Do, G Hall, ...
APS Division of Plasma Physics Meeting Abstracts 2023, PO03. 005, 2023
2023
Developing a High Energy Density Platform to Extend Measurement Windows of Hydrodynamic Instability Growth at the National Ignition Facility
S Cheng, M Burkey, K Raman, S Nagel, D Bradley, T Ebert, A Do, G Hall, ...
APS Division of Plasma Physics Meeting Abstracts 2023, PO03. 004, 2023
2023
Folded Proteins Inform the Development of Models for Intrinsically Disordered Proteins
SY Cheng, J Lincoff, S Sasmal, R Vernon, J Forman-Kay, T Head-Gordon
arXiv preprint arXiv:2007.06150, 2020
2020
Microsecond Coarse-Grained MD Simulations of Beta-Amyloid Fibrils Binding to Phase Separated Lipid Raft Domains Reveal Diverse Membrane-bounded Conformations and Binding …
K Cheng, S Cheng, Y Cao, M Rouzbehani, R Davenport-Dendy, A Urby, ...
Bulletin of the American Physical Society 65, 2020
2020
Atomistic and Coarse-Grained MD Simulation Studies of the Energetics and Interactions of Regulatory Dib1 Protein Inside a Highly Dynamic Pre-Catalytic Spliceosomal …
R Goldstein, S Cheng, G Orr, C Schreib, C Maeder, K Cheng
Bulletin of the American Physical Society 65, 2020
2020
Energetics and Interfacial Interactions of Spliceosomal Protein Dib1 Predicted with MD Simulations
R Goldstein, S Cheng, G Orr, C Schreib, K Cheng, C Maeder
The FASEB Journal 33 (S1), 627.2-627.2, 2019
2019
Computational and experimental studies of biomolecules
SY Cheng
2018
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Articles 1–20