About

Dr. Xingcheng Lin is an Assistant Professor in the Department of Physics and a member of the Bioinformatics Research Center at North Carolina State University. He serves as the Principal Investigator of the Lin Research Group, which is based at Riddick Hall in Raleigh, NC. The group includes graduate and undergraduate students from various disciplines such as Physics, Bioinformatics, Biomedical Engineering, and Aerospace Engineering, reflecting a multidisciplinary approach to research. Dr. Lin's leadership in mentoring students across these fields highlights his commitment to fostering academic growth and research development within the university community.

Research topics

• Computer Science
• Biology
• Genetics
• Artificial Intelligence
• Biophysics
• Biochemistry
• Chemistry
• Physics
• Computational biology
• Cell biology
• Chemical physics
• Combinatorial chemistry

Selected publications

• Deep learning-enabled adaptive magnetostrictive phononic crystal beams for dynamic elastic wave manipulation

  Journal of Magnetism and Magnetic Materials · 2026-04-11

  article
  PublisherDOI

• Magneto-mechanical–thermal coupling regulation of Weyl surface state topological transport in three-dimensional magnetoelastic phononic crystals

  Journal of Applied Physics · 2026-01-09

  articleOpen access1st authorCorresponding

  Weyl phononic crystals (PCs), as a key platform for topological states, feature doubly degenerate Weyl points of band structures in three-dimensional (3D) space. Their investigation has expanded from electronic systems to classical waves, including electromagnetic, acoustic, and elastic waves, and has drawn extensive attention. However, elastic wave systems are limited by fixed structures, making the active modulation of topological surface states challenging. To overcome these limitations, we design a tunable 3D Weyl magnetoelastic PC composed of magnetostrictive materials integrated with an elastic substrate. Based on the magneto-mechanical–thermal coupled constitutive relation of magnetostrictive materials, we have achieved the spatial inversion symmetry breaking under the collaborative regulation of magnetic and thermal fields, and observed the elastic wave Weyl points and their frequency-tunable characteristics. We further examine the robust transport of Weyl surface states under waveguide and defect conditions, as well as layer-selective transmission achieved through boundary condition design. This work provides a new route for dynamic regulation of elastic wave topological transport and offers significant potential for the development of customizable topological devices.

  PublisherDOI

• BPS2026 – Integrating sparse sequence, experimental, and AI-predicted structures for protein-nucleic acid interaction predictions

  Biophysical Journal · 2026-02-01

  articleSenior author
  PublisherDOI

• Author response: Active regulation of the epidermal growth factor receptor by the membrane bilayer

  2026-04-14

  peer-reviewOpen access
  PublisherDOI

• A biophysical framework for accurately identifying antigen single-amino acid escape variants and corresponding variant-specific compensatory TCR sequences

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-02-05

  articleOpen access

  ABSTRACT The impact of single amino acid substitution on T-cell receptor (TCR) recognition is central to understanding the molecular determinants of TCR specificity and degeneracy during viral mutational escape, cancer recognition, and autoimmunity. In this study, we developed a biophysics-informed computational approach integrating experimental alanine-scan mutagenesis data from the autoimmune-associated ALWGPDPAAA peptide bound to HLA-A*02:01 together with coarse-grained structural modeling. Our approach reconstructs the energetics and structural determinants underpinning the observed loss of recognition by the diabetogenic 1E6 TCR upon single-point mutations, specifically at the critical Pro 5 and Asp 6 residues. Leveraging the computational model’s ability to incorporate multiple structural templates into binding predictions, this approach quantitatively reproduces experimentally measured affinity disruptions. Additionally, we apply our approach to identify potential compensatory interactions capable of restoring binding affinity through alternative residue interactions. This integrative computational framework contributes a strategy for inferring TCR-peptide binding energetics at the single amino acid level, guiding the rational design of peptide-based immunotherapeutics, and predicting the functional impacts of clinically relevant peptide variants.

  PublisherOA PDFDOI

• Author response: Active regulation of the epidermal growth factor receptor by the membrane bilayer

  2026-01-20

  peer-reviewOpen access

  Cell surface receptors transmit information across the plasma membrane to connect the extracellular environment to intracellular function. While the structures and interactions of the receptors have been long established as mediators of signaling, increasing evidence suggests that the membrane itself plays an active role in both suppressing and enhancing signaling. Identifying and investigating this contribution has been challenging owing to the complex composition of the plasma membrane. We used cell-free expression to incorporate the epidermal growth factor receptor (EGFR) into nanodiscs with defined membrane compositions and characterized ligand-induced transmembrane conformational response and interactions with signaling partners using single-molecule and ensemble fluorescence assays. We observed that both the transmembrane conformational response and interactions with signaling partners are strongly lipid dependent, consistent with previous observations of electrostatic interactions between the anionic lipids and conserved basic residues near the membrane adjacent domain. Strikingly, the active conformation of EGFR and high levels of ATP binding were maintained regardless of ligand binding with high anionic lipid content typical of cancer cells, where EGFR signaling is enhanced. In contrast, the conformational response was suppressed in the presence of cholesterol, providing a mechanism for its known inhibitory effect on EGFR signaling. Our findings introduce a model of EGFR signaling in which the lipid environment can override ligand control, providing a biophysical basis for both robust EGFR activity in healthy cells and aberrant activity under pathological conditions. The membrane-adjacent protein sequence, likely responsible for the lipid dependence, is conserved among receptor tyrosine kinases, suggesting that active regulation by the plasma membrane may be a general feature of this important class of proteins.

  PublisherDOI

• Reviewer #1 (Public review): Active regulation of the epidermal growth factor receptor by the membrane bilayer

  2026-01-20

  peer-reviewOpen access

  Cell surface receptors transmit information across the plasma membrane to connect the extracellular environment to intracellular function. While the structures and interactions of the receptors have been long established as mediators of signaling, increasing evidence suggests that the membrane itself plays an active role in both suppressing and enhancing signaling. Identifying and investigating this contribution has been challenging owing to the complex composition of the plasma membrane. We used cell-free expression to incorporate the epidermal growth factor receptor (EGFR) into nanodiscs with defined membrane compositions and characterized ligand-induced transmembrane conformational response and interactions with signaling partners using single-molecule and ensemble fluorescence assays. We observed that both the transmembrane conformational response and interactions with signaling partners are strongly lipid dependent, consistent with previous observations of electrostatic interactions between the anionic lipids and conserved basic residues near the membrane adjacent domain. Strikingly, the active conformation of EGFR and high levels of ATP binding were maintained regardless of ligand binding with high anionic lipid content typical of cancer cells, where EGFR signaling is enhanced. In contrast, the conformational response was suppressed in the presence of cholesterol, providing a mechanism for its known inhibitory effect on EGFR signaling. Our findings introduce a model of EGFR signaling in which the lipid environment can override ligand control, providing a biophysical basis for both robust EGFR activity in healthy cells and aberrant activity under pathological conditions. The membrane-adjacent protein sequence, likely responsible for the lipid dependence, is conserved among receptor tyrosine kinases, suggesting that active regulation by the plasma membrane may be a general feature of this important class of proteins.

  PublisherDOI

• Reviewer #2 (Public review): Active regulation of the epidermal growth factor receptor by the membrane bilayer

  2026-01-20

  peer-reviewOpen access

  Cell surface receptors transmit information across the plasma membrane to connect the extracellular environment to intracellular function. While the structures and interactions of the receptors have been long established as mediators of signaling, increasing evidence suggests that the membrane itself plays an active role in both suppressing and enhancing signaling. Identifying and investigating this contribution has been challenging owing to the complex composition of the plasma membrane. We used cell-free expression to incorporate the epidermal growth factor receptor (EGFR) into nanodiscs with defined membrane compositions and characterized ligand-induced transmembrane conformational response and interactions with signaling partners using single-molecule and ensemble fluorescence assays. We observed that both the transmembrane conformational response and interactions with signaling partners are strongly lipid dependent, consistent with previous observations of electrostatic interactions between the anionic lipids and conserved basic residues near the membrane adjacent domain. Strikingly, the active conformation of EGFR and high levels of ATP binding were maintained regardless of ligand binding with high anionic lipid content typical of cancer cells, where EGFR signaling is enhanced. In contrast, the conformational response was suppressed in the presence of cholesterol, providing a mechanism for its known inhibitory effect on EGFR signaling. Our findings introduce a model of EGFR signaling in which the lipid environment can override ligand control, providing a biophysical basis for both robust EGFR activity in healthy cells and aberrant activity under pathological conditions. The membrane-adjacent protein sequence, likely responsible for the lipid dependence, is conserved among receptor tyrosine kinases, suggesting that active regulation by the plasma membrane may be a general feature of this important class of proteins.

  PublisherDOI

• FlashSchNet: Fast and Accurate Coarse-Grained Neural Network Molecular Dynamics

  Open MIND · 2026-02-13

  preprint

  Graph neural network (GNN) potentials such as SchNet improve the accuracy and transferability of molecular dynamics (MD) simulation by learning many-body interactions, but remain slower than classical force fields due to fragmented kernels and memory-bound pipelines that underutilize GPUs. We show that a missing principle is making GNN-MD IO-aware, carefully accounting for reads and writes between GPU high-bandwidth memory (HBM) and on-chip SRAM. We present FlashSchNet, an efficient and accurate IO-aware SchNet-style GNN-MD framework built on four techniques: (1) flash radial basis, which fuses pairwise distance computation, Gaussian basis expansion, and cosine envelope into a single tiled pass, computing each distance once and reusing it across all basis functions; (2) flash message passing, which fuses cutoff, neighbor gather, filter multiplication, and reduction to avoid materializing edge tensors in HBM; (3) flash aggregation, which reformulates scatter-add via CSR segment reduce, reducing atomic writes by a factor of feature dimension and enabling contention-free accumulation in both forward and backward passes; (4) channel-wise 16-bit quantization that exploits the low per-channel dynamic range in SchNet MLP weights to further improve throughput with negligible accuracy loss. On a single NVIDIA RTX PRO 6000, FlashSchNet achieves 1000 ns/day aggregate simulation throughput over 64 parallel replicas on coarse-grained (CG) protein containing 269 beads (6.5x faster than CGSchNet baseline with 80% reduction of peak memory), surpassing classical force fields (e.g. MARTINI) while retaining SchNet-level accuracy and transferability.

  DOI

• FlashSchNet: Fast and Accurate Coarse-Grained Neural Network Molecular Dynamics

  arXiv (Cornell University) · 2026-02-13

  articleOpen access

  Graph neural network (GNN) potentials such as SchNet improve the accuracy and transferability of molecular dynamics (MD) simulation by learning many-body interactions, but remain slower than classical force fields due to fragmented kernels and memory-bound pipelines that underutilize GPUs. We show that a missing principle is making GNN-MD IO-aware, carefully accounting for reads and writes between GPU high-bandwidth memory (HBM) and on-chip SRAM. We present FlashSchNet, an efficient and accurate IO-aware SchNet-style GNN-MD framework built on four techniques: (1) flash radial basis, which fuses pairwise distance computation, Gaussian basis expansion, and cosine envelope into a single tiled pass, computing each distance once and reusing it across all basis functions; (2) flash message passing, which fuses cutoff, neighbor gather, filter multiplication, and reduction to avoid materializing edge tensors in HBM; (3) flash aggregation, which reformulates scatter-add via CSR segment reduce, reducing atomic writes by a factor of feature dimension and enabling contention-free accumulation in both forward and backward passes; (4) channel-wise 16-bit quantization that exploits the low per-channel dynamic range in SchNet MLP weights to further improve throughput with negligible accuracy loss. On a single NVIDIA RTX PRO 6000, FlashSchNet achieves 1000 ns/day aggregate simulation throughput over 64 parallel replicas on coarse-grained (CG) protein containing 269 beads (6.5x faster than CGSchNet baseline with 80% reduction of peak memory), surpassing classical force fields (e.g. MARTINI) while retaining SchNet-level accuracy and transferability.

  PublisherOA PDF

Frequent coauthors

• José N. Onuchic

  Rice University

  75 shared

• Herbert Levine

  Northeastern University

  43 shared

• Nicholas P. Schafer

  Rice University

  39 shared

• Peter G. Wolynes

  Rice University

  30 shared

• Qing Yang

  Duke University

  29 shared

• Jason T. George

  Texas A&M University

  26 shared

• Bin Zhang

  25 shared

• Mingchen Chen

  23 shared

Labs

• Lin Research GroupPI

Education

• Doctor, Physics and Astronomy

  Rice University