Works (37)

Updated: March 2nd, 2024 06:14

2024 article

Explicit Ion Modeling Predicts Physicochemical Interactions for Chromatin Organization

Lin, X., & Zhang, B. (2024, January 10).

By: X. Lin*โ€‰ & B. Zhangโ€‰*

co-author countries: United States of America ๐Ÿ‡บ๐Ÿ‡ธ
Source: ORCID
Added: February 1, 2024

2024 journal article

Explicit ion modeling predicts physicochemical interactions for chromatin organization

ELife.

By: X. Lin*โ€‰ & B. Zhangโ€‰*

co-author countries: United States of America ๐Ÿ‡บ๐Ÿ‡ธ
Source: ORCID
Added: February 1, 2024

2024 journal article

Explicit ion modeling predicts physicochemical interactions for chromatin organization

ELIFE, 12.

By: X. Lin*โ€‰ & B. Zhangโ€‰*

co-author countries: United States of America ๐Ÿ‡บ๐Ÿ‡ธ
author keywords: chromatin folding; coarse-grained modeling; explicit ions; 30 nm fiber; None
Sources: ORCID, Web Of Science
Added: February 1, 2024

2023 article

Explicit Ion Modeling Predicts Physicochemical Interactions for Chromatin Organization

Lin, X., & Zhang, B. (2023, May 18).

By: X. Lin*โ€‰ & B. Zhangโ€‰*

co-author countries: United States of America ๐Ÿ‡บ๐Ÿ‡ธ
Source: ORCID
Added: February 1, 2024

2023 article

Explicit Ion Modeling Predicts Physicochemical Interactions for Chromatin Organization

Lin, X., & Zhang, B. (2023, August 21).

By: X. Lin*โ€‰ & B. Zhangโ€‰*

co-author countries: United States of America ๐Ÿ‡บ๐Ÿ‡ธ
Source: ORCID
Added: February 1, 2024

2023 article

RACER-m Leverages Structural Features for Sparse T Cell Specificity Prediction

Wang, A., Lin, X., Chau, K. N., Onuchic, J. N., Levine, H., & George, J. T. (2023, August 7). (Vol. 8). Vol. 8.

co-author countries: United States of America ๐Ÿ‡บ๐Ÿ‡ธ
Source: ORCID
Added: February 1, 2024

2023 article

Single-molecule acceptor rise time (smART) FRET for nanoscale distance sensitivity

Guo, J., Chen, X., Manna, P., Lin, X., Scott, M. N., Chen, W. J., โ€ฆ Schlau-Cohen, G. S. (2023, March 16).

co-author countries: China ๐Ÿ‡จ๐Ÿ‡ณ Israel ๐Ÿ‡ฎ๐Ÿ‡ฑ United States of America ๐Ÿ‡บ๐Ÿ‡ธ
Source: ORCID
Added: April 5, 2023

2022 journal article

Chromatin fiber breaks into clutches under tension and crowding

Nucleic Acids Research, 50(17), 9738โ€“9747.

By: S. Liuโ€‰*, X. Lin*โ€‰ & B. Zhangโ€‰*

co-author countries: United States of America ๐Ÿ‡บ๐Ÿ‡ธ
MeSH headings : Cell Nucleus; Chromatin; Molecular Conformation; Nucleosomes
Sources: ORCID, Crossref
Added: April 5, 2023

2022 journal article

Contact map dependence of a T-cell receptor binding repertoire

Physical Review E.

co-author countries: United States of America ๐Ÿ‡บ๐Ÿ‡ธ
Source: ORCID
Added: April 5, 2023

2022 journal article

Ligand-induced transmembrane conformational coupling in monomeric EGFR

Nature Communications, 13(1).

co-author countries: France ๐Ÿ‡ซ๐Ÿ‡ท United Kingdom of Great Britain and Northern Ireland ๐Ÿ‡ฌ๐Ÿ‡ง United States of America ๐Ÿ‡บ๐Ÿ‡ธ
MeSH headings : Cell Membrane / metabolism; ErbB Receptors / metabolism; Ligands; Protein Binding; Protein Conformation
Sources: ORCID, Crossref
Added: April 5, 2023

2021 article

Chromatin fiber breaks into clutches under tension and crowding

Liu, S., Lin, X., & Zhang, B. (2021, November 18). (Vol. 11). Vol. 11.

By: S. Liu*, X. Lin*โ€‰ & B. Zhang

co-author countries: United States of America ๐Ÿ‡บ๐Ÿ‡ธ
Source: ORCID
Added: February 1, 2024

2021 journal article

Cooperative DNA looping by PRC2 complexes

Nucleic Acids Research, 49(11), 6238โ€“6248.

co-author countries: United States of America ๐Ÿ‡บ๐Ÿ‡ธ
Sources: ORCID, Crossref
Added: April 5, 2023

2021 journal article

Exploring Energy Landscapes of Intrinsically Disordered Proteins: Insights into Functional Mechanisms

Journal of Chemical Theory and Computation, 17(5), 3178โ€“3187.

By: A. Oliveira Junior, X. Lin*โ€‰, P. Kulkarniโ€‰*, J. Onuchicโ€‰*, S. Royโ€‰* & V. Leiteโ€‰*

co-author countries: Brazil ๐Ÿ‡ง๐Ÿ‡ท India ๐Ÿ‡ฎ๐Ÿ‡ณ United States of America ๐Ÿ‡บ๐Ÿ‡ธ
MeSH headings : Amino Acid Sequence; Intrinsically Disordered Proteins / chemistry; Intrinsically Disordered Proteins / metabolism; Phosphorylation; Protein Conformation; Protein Isoforms / chemistry; Protein Isoforms / metabolism; Reproducibility of Results; Sequence Homology, Amino Acid
Sources: ORCID, Crossref
Added: April 5, 2023

2021 article

Ligand-induced transmembrane conformational coupling in monomeric EGFR

Srinivasan, S., Regmi, R., Lin, X., Dreyer, C. A., Chen, X., Quinn, S. D., โ€ฆ Schlau-Cohen, G. S. (2021, October 28). (Vol. 10). Vol. 10.

co-author countries: United States of America ๐Ÿ‡บ๐Ÿ‡ธ
Source: ORCID
Added: February 1, 2024

2021 journal article

Multiscale modeling of genome organization with maximum entropy optimization

The Journal of Chemical Physics, 155(1), 010901.

co-author countries: United States of America ๐Ÿ‡บ๐Ÿ‡ธ
MeSH headings : Algorithms; DNA / genetics; Entropy; Humans; Models, Genetic; Molecular Dynamics Simulation
Sources: ORCID, Crossref
Added: April 5, 2023

2021 journal article

Rapid assessment of T-cell receptor specificity of the immune repertoire

Nature Computational Science, 1(5), 362โ€“373.

co-author countries: United States of America ๐Ÿ‡บ๐Ÿ‡ธ
Sources: Crossref, ORCID
Added: April 7, 2023

2021 journal article

Rapid assessment of T-cell receptor specificity of the immune repertoire

Nature Computational Science.

Contributors: X. Lin*โ€‰

Source: ORCID
Added: February 1, 2024

2021 journal article

Stability and folding pathways of tetra-nucleosome from six-dimensional free energy surface

Nature Communications, 12(1).

By: X. Dingโ€‰*, X. Lin*โ€‰ & B. Zhangโ€‰*

co-author countries: United States of America ๐Ÿ‡บ๐Ÿ‡ธ
MeSH headings : Acetylation; Algorithms; Animals; Chromatin / chemistry; Chromatin / genetics; Chromatin / metabolism; DNA / chemistry; DNA / genetics; DNA / metabolism; Histones / chemistry; Histones / metabolism; Humans; Models, Molecular; Nucleic Acid Conformation; Nucleosomes / chemistry; Nucleosomes / genetics; Nucleosomes / metabolism; Protein Conformation; Thermodynamics
Sources: ORCID, Crossref
Added: April 5, 2023

2020 journal article

Enhancing intracellular accumulation and target engagement of PROTACs with reversible covalent chemistry

Nature Communications, 11(1).

co-author countries: United States of America ๐Ÿ‡บ๐Ÿ‡ธ

Contributors: X. Lin*โ€‰

MeSH headings : Acrylamides / chemistry; Adaptor Proteins, Signal Transducing / metabolism; Agammaglobulinaemia Tyrosine Kinase / genetics; Agammaglobulinaemia Tyrosine Kinase / metabolism; Cell Line; Cell Survival; Fluorescent Dyes; Half-Life; Humans; Intracellular Space / metabolism; Ligands; Molecular Dynamics Simulation; Mutation; Organic Chemistry Phenomena; Protein Binding; Protein Interaction Domains and Motifs; Proteolysis; Ubiquitin-Protein Ligases / metabolism
Sources: ORCID, Crossref
Added: April 5, 2023

2020 journal article

Molecular-replacement phasing using predicted protein structures from AWSEM-Suite

IUCrJ, 7(6), 1168โ€“1178.

By: S. Jinโ€‰*, M. Millerโ€‰*, M. Chen*, N. Schafer*, X. Lin*โ€‰, X. Chenโ€‰*, G. Phillips*, P. Wolynesโ€‰*

co-author countries: United States of America ๐Ÿ‡บ๐Ÿ‡ธ
Sources: ORCID, Crossref
Added: April 5, 2023

2020 journal article

Protein Structure Prediction in CASP13 Using AWSEM-Suite

Journal of Chemical Theory and Computation, 16(6), 3977โ€“3988.

co-author countries: United States of America ๐Ÿ‡บ๐Ÿ‡ธ
MeSH headings : Algorithms; Humans; Molecular Dynamics Simulation / standards; Protein Conformation; Protein Folding; Proteins / chemistry
Sources: ORCID, Crossref
Added: April 5, 2023

2020 journal article

Protein Structure Refinement Guided by Atomic Packing Frustration Analysis

The Journal of Physical Chemistry B, 124(48), 10889โ€“10898.

co-author countries: United States of America ๐Ÿ‡บ๐Ÿ‡ธ
MeSH headings : Computational Biology; Machine Learning; Molecular Dynamics Simulation; Protein Conformation; Protein Folding; Proteins
Sources: Crossref, ORCID
Added: April 6, 2023

2020 journal article

Single-molecule and in silico dissection of the interaction between Polycomb repressive complex 2 and chromatin

Proceedings of the National Academy of Sciences, 117(48), 30465โ€“30475.

co-author countries: United States of America ๐Ÿ‡บ๐Ÿ‡ธ
MeSH headings : Chromatin / chemistry; Chromatin / genetics; Chromatin / metabolism; Epigenesis, Genetic; Heterochromatin / genetics; Histones / metabolism; Humans; Methylation; Models, Biological; Models, Molecular; Molecular Dynamics Simulation; Mutation; Nucleosomes; Polycomb Repressive Complex 2 / chemistry; Polycomb Repressive Complex 2 / metabolism; Protein Binding; Protein Conformation; Single Molecule Imaging / methods; Spectrum Analysis; Structure-Activity Relationship
Sources: ORCID, Crossref
Added: April 5, 2023

2019 journal article

Forging tools for refining predicted protein structures

Proceedings of the National Academy of Sciences, 116(19), 9400โ€“9409.

co-author countries: United States of America ๐Ÿ‡บ๐Ÿ‡ธ
MeSH headings : Crystallography, X-Ray; Models, Molecular; Protein Conformation; Proteins / chemistry; Software
Sources: ORCID, Crossref
Added: April 5, 2023

2019 journal article

Recent Advances in Computational Protocols Addressing Intrinsically Disordered Proteins

Biomolecules, 9(4), 146.

By: S. Bhattacharyaโ€‰* & X. Lin*โ€‰

co-author countries: United States of America ๐Ÿ‡บ๐Ÿ‡ธ
MeSH headings : Animals; Drug Discovery / methods; Humans; Intrinsically Disordered Proteins / antagonists & inhibitors; Intrinsically Disordered Proteins / chemistry; Intrinsically Disordered Proteins / metabolism; Molecular Docking Simulation / methods; Molecular Dynamics Simulation; Small Molecule Libraries / chemistry; Small Molecule Libraries / pharmacology
Sources: ORCID, Crossref
Added: April 5, 2023

2019 journal article

Structural and Dynamical Order of a Disordered Protein: Molecular Insights into Conformational Switching of PAGE4 at the Systems Level

Biomolecules, 9(2), 77.

By: X. Lin*โ€‰, P. Kulkarniโ€‰*, F. Bocciโ€‰*, N. Schafer*, S. Royโ€‰*, M. Tsaiโ€‰*, Y. Heโ€‰*, Y. Chenโ€‰* ...

co-author countries: Canada ๐Ÿ‡จ๐Ÿ‡ฆ China ๐Ÿ‡จ๐Ÿ‡ณ India ๐Ÿ‡ฎ๐Ÿ‡ณ Russian Federation ๐Ÿ‡ท๐Ÿ‡บ Taiwan, Province of China ๐Ÿ‡น๐Ÿ‡ผ United States of America ๐Ÿ‡บ๐Ÿ‡ธ
author keywords: PAGE4; intrinsically disordered proteins; conformational plasticity; order-disorder transition; phosphorylation
MeSH headings : Antigens, Neoplasm / chemistry; Antigens, Neoplasm / metabolism; Humans; Intrinsically Disordered Proteins / chemistry; Intrinsically Disordered Proteins / metabolism; Molecular Dynamics Simulation; Protein Conformation
Sources: ORCID, Crossref, Web Of Science
Added: March 25, 2019

2018 journal article

Atomistic simulations indicate the functional loop-to-coiled-coil transition in influenza hemagglutinin is not downhill

Proceedings of the National Academy of Sciences, 115(34).

co-author countries: Germany ๐Ÿ‡ฉ๐Ÿ‡ช United States of America ๐Ÿ‡บ๐Ÿ‡ธ
MeSH headings : Hemagglutinin Glycoproteins, Influenza Virus / chemistry; Hemagglutinin Glycoproteins, Influenza Virus / metabolism; Influenza A virus / chemistry; Influenza A virus / metabolism; Molecular Dynamics Simulation; Protein Structure, Quaternary; Protein Structure, Secondary
Sources: ORCID, Crossref
Added: April 5, 2023

2018 journal article

PAGE4 and Conformational Switching: Insights from Molecular Dynamics Simulations and Implications for Prostate Cancer

Journal of Molecular Biology, 430(16), 2422โ€“2438.

By: X. Lin*โ€‰, S. Royโ€‰*, M. Jolly*, F. Bocciโ€‰*, N. Schafer*, M. Tsaiโ€‰*, Y. Chenโ€‰*, Y. Heโ€‰* ...

co-author countries: India ๐Ÿ‡ฎ๐Ÿ‡ณ United States of America ๐Ÿ‡บ๐Ÿ‡ธ

Contributors: X. Lin*โ€‰, S. Royโ€‰*, M. Jolly*, F. Bocciโ€‰*, N. Schafer*, M. Tsaiโ€‰*, Y. Chenโ€‰*, Y. Heโ€‰* ...

author keywords: intrinsically disordered protein; PAGE4; AWSEM; order-disorder transition; non-genetic heterogeneity
MeSH headings : Antigens, Neoplasm / chemistry; Antigens, Neoplasm / metabolism; Fluorescence Resonance Energy Transfer; Humans; Male; Models, Molecular; Models, Theoretical; Molecular Dynamics Simulation; Phosphorylation; Prostatic Neoplasms / metabolism; Protein Conformation; Protein Serine-Threonine Kinases / metabolism; Protein-Tyrosine Kinases / metabolism; Receptors, Androgen / metabolism; Scattering, Small Angle; Signal Transduction; Single Molecule Imaging; Transcription Factor AP-1 / metabolism; X-Ray Diffraction
Sources: ORCID, Crossref
Added: February 5, 2020

2018 article

PAGE4 and Conformational Switching: Insights from Molecular Dynamics Simulations and Implications for Prostate Cancer

Lin, X., Roy, S., Jolly, M. K., Bocci, F., Schafer, N., Tsai, M.-Y., โ€ฆ Onuchic, J. N. (2018, February 14). (Vol. 2). Vol. 2.

co-author countries: India ๐Ÿ‡ฎ๐Ÿ‡ณ United States of America ๐Ÿ‡บ๐Ÿ‡ธ
Source: ORCID
Added: February 1, 2024

2018 journal article

Template-Guided Protein Structure Prediction and Refinement Using Optimized Folding Landscape Force Fields

Journal of Chemical Theory and Computation, 14(11), 6102โ€“6116.

co-author countries: United States of America ๐Ÿ‡บ๐Ÿ‡ธ
MeSH headings : Models, Molecular; Protein Conformation; Protein Folding; Proteins / chemistry
Sources: ORCID, Crossref
Added: April 5, 2023

2017 journal article

Quantum Image Processing and Its Application to Edge Detection: Theory and Experiment

Physical Review X, 7(3).

By: X. Yao*, H. Wangโ€‰*, Z. Liaoโ€‰*, M. Chen*, J. Pan*, J. Liโ€‰*, K. Zhang*, X. Lin*โ€‰ ...

co-author countries: China ๐Ÿ‡จ๐Ÿ‡ณ Germany ๐Ÿ‡ฉ๐Ÿ‡ช United States of America ๐Ÿ‡บ๐Ÿ‡ธ

Contributors: X. Yao*, H. Wangโ€‰*, Z. Liaoโ€‰*, M. Chen*, J. Pan*, J. Liโ€‰*, K. Zhang*, X. Lin*โ€‰ ...

Sources: ORCID, Crossref
Added: April 5, 2023

2016 journal article

Lowered pH Leads to Fusion Peptide Release and a Highly Dynamic Intermediate of Influenza Hemagglutinin

The Journal of Physical Chemistry B, 120(36), 9654โ€“9660.

co-author countries: Germany ๐Ÿ‡ฉ๐Ÿ‡ช United States of America ๐Ÿ‡บ๐Ÿ‡ธ
MeSH headings : Hemagglutinin Glycoproteins, Influenza Virus / chemistry; Humans; Hydrogen-Ion Concentration; Influenza, Human; Molecular Dynamics Simulation; Peptides / chemistry; Protons
Sources: ORCID, Crossref
Added: April 5, 2023

2016 journal article

Protein Folding and Structure Prediction from the Ground Up II: AAWSEM for ฮฑ/ฮฒ Proteins

The Journal of Physical Chemistry B, 121(15), 3473โ€“3482.

By: M. Chenโ€‰*, X. Lin*โ€‰, W. Luโ€‰*, J. Onuchicโ€‰* & P. Wolynes*

co-author countries: United States of America ๐Ÿ‡บ๐Ÿ‡ธ

Contributors: M. Chenโ€‰*, X. Lin*โ€‰, W. Luโ€‰*, J. Onuchicโ€‰* & P. Wolynes*

MeSH headings : Molecular Dynamics Simulation; Protein Conformation; Protein Folding; Proteins / chemistry; Thermodynamics
Sources: ORCID, Crossref
Added: April 5, 2023

2016 journal article

Protein Folding and Structure Prediction from the Ground Up: The Atomistic Associative Memory, Water Mediated, Structure and Energy Model

The Journal of Physical Chemistry B, 120(33), 8557โ€“8565.

By: M. Chenโ€‰*, X. Lin*โ€‰, W. Zheng*, J. Onuchicโ€‰* & P. Wolynes*

co-author countries: United States of America ๐Ÿ‡บ๐Ÿ‡ธ

Contributors: M. Chenโ€‰*, X. Lin*โ€‰, W. Zheng*, J. Onuchicโ€‰* & P. Wolynes*

MeSH headings : Algorithms; Cluster Analysis; Computer Simulation; Models, Molecular; Myoglobin / chemistry; Myoglobin / metabolism; Protein Folding; Protein Structure, Secondary; Solvents / chemistry; Water / chemistry
Sources: ORCID, Crossref
Added: April 5, 2023

2014 journal article

Order and disorder control the functional rearrangement of influenza hemagglutinin

Proceedings of the National Academy of Sciences, 111(33), 12049โ€“12054.

co-author countries: United States of America ๐Ÿ‡บ๐Ÿ‡ธ
MeSH headings : Hemagglutinin Glycoproteins, Influenza Virus / chemistry; Molecular Dynamics Simulation
Sources: ORCID, Crossref
Added: April 5, 2023

2010 journal article

Measurement method of logical gate in bulk spin quantum computer

Wuhan Ligong Daxue Xuebao/Journal of Wuhan University of Technology, 32(15), 142โ€“145.

By: X. Yao, Z. Chen, X. Mu, J. Pan, C. Yang, X. Linโ€‰, J. Lian, X. Wang

Contributors: X. Yao, Z. Chen, X. Mu, J. Pan, C. Yang, X. Linโ€‰, J. Lian, X. Wang

Source: ORCID
Added: April 5, 2023

2010 journal article

Subspace quantum process tomography via nuclear magnetic resonance

Acta Physica Sinica, 59(10), 6837.

By: Z. Bi-Rong, L. Qin, M. Xiao-Yang, L. Xing-Cheng, Y. Chun, P. Jian, C. Zhong

Sources: Crossref, ORCID
Added: April 7, 2023

Employment

Updated: July 20th, 2023 10:51

2023 - present

North Carolina State University Raleigh, North Carolina, US
Assistant Professor Physics

2018 - 2023

Massachusetts Institute of Technology Cambridge, MA, US
Postdoctoral Associate Chemistry

2018 - 2018

Rice University Houston, TX, US
Postdoctoral Researcher Center for Theoretical Biological Physics

Education

Updated: February 11th, 2018 23:45

2011 - present

Rice University Houston, TX, US
Doctor Physics and Astronomy

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