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<!doctype html>
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<title>Research — Yifang Chen</title>
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<span class="avatar" aria-hidden="true">YC</span>
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<h1>Yifang Chen</h1>
<p>Molecular dynamics · Enhanced sampling · Markov state models · ML/DL</p>
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<section class="section">
<h2>Research Overview</h2>
<p class="lead">
I’ve worked across both experimental and computational research. On the experimental side:
organic synthesis for peptide hydrogels, and inorganic/organometallic nanomaterials.
On the computational side: multiscale simulations of protein–protein, protein–peptide,
protein–ligand, glycogen–enzyme, and membrane–protein systems.
I currently focus on chromatin dynamics using a coarse-grained model implemented in OpenMM within our group.
</p>
</section>
<section class="section">
<h2>Publications</h2>
<ul>
<li>
Tiankuo Wang, Yiran Li, Juan Wang, Ying Xu, <strong>Yifang Chen</strong>, Zilin Lu, Wei Wang, Bin Xue*, Ying Li*, Yi Cao*,
<em>Smart Adhesive Peptide Nanofibers for Cell Capture and Release</em>,
<span class="small"><cite>ACS Biomaterials Science & Engineering</cite></span>.
<a href="https://doi.org/10.1021/acsbiomaterials.0c01485" target="_blank" rel="noopener noreferrer">https://doi.org/10.1021/acsbiomaterials.0c01485</a>
</li>
<li>
Hui He, <strong>Yifang Chen</strong>, Faping Wang, Xue Liu, Yan Guo*,
<em>Nitrite Sensing Behaviours of Tailored Bimetallic Oxide CuMnO<sub>2</sub> Nanostructures</em>,
<span class="small"><cite>Journal of Materials Science: Materials in Electronics</cite></span>.
<a href="https://doi.org/10.1007/s10854-021-07390-4" target="_blank" rel="noopener noreferrer">https://doi.org/10.1007/s10854-021-07390-4</a>
</li>
<li>
Yan Guo, <strong>Yifang Chen</strong>, Xiaoxi Hu, Yuan Yao, Zhuang Li,
<em>Tween-Modified CuFe<sub>2</sub>O<sub>4</sub> Nanoparticles with Enhanced Supercapacitor Performance</em>,
<span class="small"><cite>Colloids and Surfaces A: Physicochemical and Engineering Aspects</cite></span>.
<a href="https://doi.org/10.1016/j.colsurfa.2021.127676" target="_blank" rel="noopener noreferrer">https://doi.org/10.1016/j.colsurfa.2021.127676</a>
</li>
<li>
Huiyi Guan<sup>1,2†</sup>, Huan Chen<sup>1,2†</sup>, He Geng<sup>1,2†</sup>, Ruifang Ma<sup>1,2</sup>, Zhongmin Liu<sup>2</sup>,
Yong Wang<sup>3</sup>, <strong>Yifang Chen<sup>3*</sup></strong>, Kaige Yan<sup>1,2,4*</sup>,
<em>Molecular architecture and catalytic mechanism of human glycogen debranching enzyme</em>,
<span class="small"><cite>Nature Communications</cite></span>.
<a href="https://doi.org/10.1038/s41467-025-61077-6" target="_blank" rel="noopener noreferrer">https://doi.org/10.1038/s41467-025-61077-6</a>
</li>
<li>
Bowen Du<sup>1,†</sup>, Ruifang Ma<sup>1,†</sup>, Lili Cheng<sup>2,†</sup>, <strong>Yifang Chen<sup>3,†</sup></strong>,
Yong Wang<sup>3*</sup>, Ligong Chen<sup>2*</sup>, Kaige Yan<sup>1,5*</sup>,
<em>Structural Insights into Substrate Recognition and Inhibition of the Creatine Transporter CT1</em>,
<span class="small">under review</span>
</li>
<li>
Xi Liu<sup>1,†</sup>, <strong>Yifang Chen<sup>2,11†</sup></strong>, Likun Wang<sup>3,†</sup>, Qunlong Zhang<sup>4,5</sup>, Lingyu Jiang<sup>6</sup>, Lu Xu<sup>6</sup>
Yechen Liu<sup>1</sup>, Li Jiao<sup>6</sup>, Ruming Liu<sup>6</sup>, Sha Sun<sup>7</sup>, Zhaoyong Lu<sup>4,8,9*</sup>, Wei Zheng<sup>3,8*</sup>, Yong Wang<sup>2,10*</sup>, Xin Bian<sup>1,8*</sup>,
<em>Molecular basis and function of scramblase VMP1 in complex with lipid transfer protein ATG2A</em>,
<span class="small">in progress</span>
</li>
<li>
Kieran Russell<sup>1,2</sup>, <strong>Yifang Chen<sup>1</sup></strong>, Jorge R. Espinosa<sup>1,2,3</sup>, David Farre-Gil<sup>4,5</sup>,
Huabing Zhou<sup>2,6</sup>, Maria Julia Maristany<sup>1,2</sup>, Jose Ignacio Perez-Lopez<sup>1,2</sup>, Jan Huertas<sup>1,2,7</sup>, Modesto Orozco<sup>4,8*</sup>, Michael K. Rosen<sup>2,6*</sup>, Rosana Collepardo-Guevara<sup>1,2,7*</sup>,
<em>Near-atomistic simulations reveal the molecular principles that control chromatin structure and phase separation</em>,
<span class="small">BioRxiv</span>
</li>
</ul>
<p class="small">† equal contribution; * corresponding author.</p>
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