Curriculum Vitae - Xubo Lin

1/9

Xubo Lin (林绪波), Ph.D.

Tenure-track Associate Professor (University 100-Talent Program), Beijing Advanced

Innovation Center for Biomedical Engineering, Beihang University (BUAA), Beijing, China

Gender: Male; Birthday: December, 1986

Phone: +86-15510029836

Email: linxbseu@buaa.edu.cn or Linxbseu@163.com

Personal homepage: http://linxubo.weebly.com/

Google Scholar: https://goo.gl/YC16pj

RESEARCH INTERESTS

Membrane Biophysics

Nano-Bio Interface

Coarse-grained and All-atom Molecular Dynamics Simulation

Free Energy Calculation and Enhanced Sampling Methods

Computational Biology

Cell Biology and Molecular Biology

EDUCATION 09/2009-09/2014 Ph.D. in Biomedical Engineering, School of Biological Science & Medical Engineering,

Southeast University, Nanjing, China (Supervisor: Dr. Ning Gu)

09/2005-07/2009 B.Sc. in Applied Physics, Department of Physics, Southeast University, Nanjing, China

RESEARCH EXPERIENCES 01/22/2018~now Tenure-track Associate Professor (University 100-Talent Program, Nanobiology &

Membrane Biophysics), Beijing Advanced Innovation Center for Biomedical Engineering, Beihang University (BUAA), Beijing, China

10/2014~11/2017 Postdoctoral Fellow (Membrane Biophysics), Department of Integrative Biology & Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston. Primary Mentor: Dr. Alemayehu Gorfe (Computational experts); Secondary Mentor: Dr. Ilya Levental (Experimental experts).

Curriculum Vitae - Xubo Lin

2/9

07/2017~07/2017 Visiting Postdoc (Structural Bioinformatics), Complex Systems Division, Beijing Computational Science Research Center, Beijing, China. Supervisor: Dr. Haiguang Liu

09/2009-09/2014 Graduate Student (Nanobiophysics & Membrane), School of Biological Science & Medical Engineering, Southeast University, Nanjing, China. Supervisor: Dr. Ning Gu (Yangtze River Scholar Professor).

06/2014-07/2014 Visiting Graduate Student, Macromolecular dynamics: structure, function and diseases (KITPC program), Kavli Institute for Theoretical Physics China at the Chinese Academy of Sciences (KITPC), Beijing, China. Lectures on the research frontiers of Macromolecular Dynamics

06/2013-12/2013 Visiting Graduate Student, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing, China Supervisor: Dr. Xianming Kong and Dr. Yi Y. Zuo Biophysical study of the interactions of nanoparticles with self-assembled

monolayers using Langmuir-Blodgett Trough and AFM 05/2012-06/2012 Visiting Graduate Student, Membrane Biophysics | Theory and Experiment (KITPC

program), Kavli Institute for Theoretical Physics China at the Chinese Academy of Sciences (KITPC), Beijing, China. Lectures on the research frontiers of Membrane Biophysics

12/2011-01/2012 Visiting Graduate Student, Soft Matter Mechanics Summer School 2011, Zhejiang University, Hangzhou, China. Lectures on the research frontiers of Soft Matter

07/2011-07/2011 Visiting Graduate Student, The BME Leader Training Summer School 2011, Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, China. Lectures on the research frontiers of Biomedical Engineering and professional

training on writing grant proposal 09/2005-07/2009 Undergraduate Student, Department of Physics, Southeast University, Nanjing, China

Thermodynamics, Theoretical Physics, Optics, Interface, etc.

SCHOLARSHIPS AND AWARDS 2018 Outstanding Young Researcher Award of the workshop “From Computational Biophysics to

Systems Biology (CBSB2018)” 2016 Education Committee Travel Award of American Biophysical Society 60th Annual Meeting 2015 Contributed Talk Award and Travel Award of the workshop “From Computational Biophysics to

Curriculum Vitae - Xubo Lin

3/9

Systems Biology (CBSB2015)” 2013 Star of the Year, Biological and Medical Nanotechnology Group, Southeast University 2012 National Scholarship for PhD student, Southeast University 2012 CASC First-level Scholarship, Southeast University 2011 Young Scientist Travel Award and Best Poster Award of 17th International Biophysics Congress 2011 Scholarship Award for Excellent Doctoral Student granted by Ministry of Education 2009-2010 Master Students’ First-level Scholarship, Southeast University 2009 Outstanding Graduate, Southeast University 2008 National Inspirational Scholarships for undergraduate student, Southeast University 2006 National Scholarship for undergraduate student, Southeast University

GRANTS

* PI: Principal Investigator; TACC: Texas Advanced Computing Center; XSEDE: The NSF Extreme Science and

Engineering Discovery Environment; PSC: Pittsburgh Supercomputing Center.

* Stampede, Lonestar5, and Lonestar are supercomputing clusters in TACC, while Maverick is the computing cluster

designed for visualization. SU is the unit for computational resources. Lonestar5 uses node (24 cores)-hour for SU, while

others use core-hour for SU. The value of SU is about $0.036 per core-hour. Anton2 is the fastest supercomputer specifically

for molecular dynamics simulations, which is maintained by PSC.

As a PI:

2018~2021, PI: Dr. Xubo Lin, 6th Youth Talent Plan of Beihang University (BUAA): RMB 1,000,000.

2018~2020, PI: Dr. Xubo Lin, Startup Fund of Beijing Advanced Innovation Center for Biomedical

Engineering, Beihang University (BUAA): RMB 300,000.

2014~2017, PI: Dr. Xubo Lin, TACC (G-816078), “The Interactions between Nanoparticles and Cell

Membrane”: 1,850,000 SUs (Stampede), 23,300 SUs (Lonestar5), 875,000 SUs (Lonestar).

2015~2017, PI: Dr. Xubo Lin, TACC (G-816395), “The Effects of Polyunsaturated Fatty Acids on the

Dynamics of Lipid Raft”: 675,000 SUs (Stampede), 20,834 SUs (Lonestar5), 1,200,000 SUs (Lonestar), 6,000

SUs (Maverick).

As a Participant:

2014~2015, PI: Dr. Alemayehu Gorfe, TACC (G-815830), “Modeling Membrane-Bound Ras Dimers”:

1,150,000 SUs (Stampede).

2015~2017, PI: Dr. Alemayehu Gorfe, XSEDE (TG-MCB150054), “Investigation of surface-bound and trans-

membrane proteins with molecular dynamics simulations: Structure, dynamics, oligomerization and ligand

design”: 5,597,686 SUs (Stampede, TACC), 2,291,700 SUs (Comet, SDSC).

2016~2017, PI: Dr. Alemayehu Gorfe, PSC (PSCA16072P), “Membrane reorientation and assembly of K-

Ras”: 291,000 MDUs (Anton2).

Participated in National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

grant (No. RO1 GM100078, 2012-2017) and Cancer Prevention and Research Institute of Texas (CPRIT) grant

(No. DP150093, 2015-2017) with Dr. Alemayehu Gorfe as the Principal Investigator.

Curriculum Vitae - Xubo Lin

4/9

Participated in NIH/NIGMS grant (No. R01 GM114282, 2015-2020) and CPRIT First-Time, Tenure-Track

Faculty grant (No. R1215, 2012-2017) with Dr. Ilya Levental as the Principal Investigator.

Participated in the National Important Basic Research Program of China (No. 2006CB933206 and

2011CB933503) and the National Natural Science Foundation of China (Nos. 60725101 and 61127002) with

Dr. Ning Gu as the Principal Investigator (2009~2014).

PUBLICATIONS

Journal Papers (# Contribute equally; * Corresponding Author; Journal Ranking: Q1, Q2…)

Summary: 25 papers published in Nature Communications, Nanoscale, Nano Research,

Soft Matter, Biophysical Journal, Journal of Physical Chemistry B/C, FEBS Letters,

Colloids and Surfaces B: Biointerfaces, etc. with 342 total citations (Google Scholar, h-

index=11) as well as 2 book chapters.

Work @ BUAA (2018~now):

[1] Xubo Lin* and Alemayehu A. Gorfe*. Understanding Membrane Domain-Partitioning Thermodynamics of

Transmembrane Domains with Potential of Mean Force Calculations. Journal of Physical Chemistry B, 2019,

DOI: 10.1021/acs.jpcb.8b10148. (Q2)

[2] Yang Wang#, Cecylia Severin Lupala#, Haiguang Liu*, Xubo Lin*. Identification of Drug Binding Sites and

Action Mechanisms with Molecular Dynamics Simulations. Current Topics in Medicinal Chemistry, 2018,

18, 2268-2277. (Q2, Invited Review)

[3] Xubo Lin, Hongyin Wang#, Zhichao Lou#, Meng Cao#, Zuoheng Zhang, Ning Gu*. Roles of PIP2 in the

membrane binding of MIM I-BAR: insights from molecular dynamics simulations. FEBS Letters, 2018, 592,

2533-2542. (Q2)

[4] Xubo Lin, Vinay Nair, Yong Zhou, Alemayehu A. Gorfe*. Membrane Potential and Dynamics in a Ternary

Lipid Mixture: Insights from Molecular Dynamics Simulations. Physical Chemistry Chemical Physics, 2018,

20, 15841-15851. (Q1)

[5] Xubo Lin, Alemayehu A. Gorfe*, Ilya Levental*. Protein Partitioning into Ordered Membrane Domains:

Insights from Simulations. Biophysical Journal, 2018, 114, 1936-1944. (Q1)

Before joining BUAA (2010-2017):

[6] Joseph H. Lorent, Barbara Diaz-Rohrer, Xubo Lin, Kevin Spring, Alemayehu A. Gorfe, Kandice R. Levental,

Ilya Levental*. Structural determinants and functional consequences of protein affinity for membrane rafts.

Nature Communications, 2017, 8, 1219. (Q1)

[7] Zuoheng Zhang#, Xubo Lin#, Ning Gu*. Effects of Temperature and PEG Density on the Translocation of

Curriculum Vitae - Xubo Lin

5/9

PEGylated Nanoparticles across Asymmetric Lipid Membrane. Colloids and Surfaces B: Biointerfaces, 2017,

160, 92-100. (Q1)

[8] Yue Zhang, Zhichao Lou, Xubo Lin, Qiwei Wang, Meng Cao, Ning Gu*. Optimizing purification process

of MIM-I-BAR domain by introducing atomic force microscope and dynamics simulations. Colloids and

Surfaces B: Biointerfaces, 2017, 157, 391-397. (Q1)

[9] Hui Ding, Xianhua Gui, Xubo Lin, Ruhua Chen, Tieliang Ma, Yunlu Sheng*, Hourong Cai*, Yan Fen*. The

Prognostic Effect of MAC30 Expression on Patients with Non-Small Cell Lung Cancer Receiving Adjuvant

Chemotherapy. Technology in Cancer Research & Treatment, 2017, 16, 645-653. (Q3)

[10] Xubo Lin, Joseph H. Lorent, Allison D. Skinkle, Kandice R. Levental, M. Neal Waxham, Alemayehu A.

Gorfe*, Ilya Levental*. Domain Stability in Biomimetic Membranes Driven by Lipid Polyunsaturation.

Journal of Physical Chemistry B, 2016, 120, 11930-11941. (Q2)

[11] Xubo Lin#, Siya Zhang#, Hui Ding, Ilya Levental*, Alemayehu A. Gorfe*. The aliphatic chain of cholesterol

modulates bilayer interleaflet coupling and domain registration. FEBS Letters, 2016, 590, 3368-3374. (Q2)

[12] Dandan Sun, Xubo Lin, Zuoheng Zhang, Ning Gu*. Impact of Shock-induced Lipid Nanobubble Collapse

on a Phospholipid Membrane. Journal of Physical Chemistry C, 2016, 120, 18803-18810. (Q1)

[13] Kandice R. Levental, Joseph H. Lorent, Xubo Lin, Allison Skinkle, Michal Surma, Emily Stockenbojer,

Alemayehu A. Gorfe, Ilya Levental*. Polyunsaturated lipids regulate membrane domain stability by tuning

membrane order. Biophysical Journal, 2016, 110, 1800-1810. (Q1)

[14] Hui Ding, Xianhua Gui, Xubo Lin, Ruhua Chen, Hourong Cai, Yan Fen, Yunlu Sheng. Prognostic Value of

MAC30 Expression in Human Pure Squamous Cell Carcinomas of the Lung. Asian Pacific Journal of Cancer

Prevention, 2016, 17, 2705-2710. (Q3)

[15] Ruhua Chen, Yan Fen, Xubo Lin, Tieliang Ma, Hourong Cai, Hui Ding*. Overexpression of MAC30 is

Resistant to Platinum-Based Chemotherapy in Patients with Non-Small Cell Lung Cancer. Technology in

Cancer Research & Treatment, 2016, 15, 815-820. (Q3)

[16] Xubo Lin, Zhenlong Li, Alemayehu A. Gorfe*. Reversibility of the effects of peptide concentration and lipid

composition on the clustering of H-Ras lipid anchors. Biophysical Journal, 2015, 109, 2467-2470. (Q1)

[17] Xubo Lin, Yi Y. Zuo, Ning Gu*. Shape Affects the Interactions of Nanoparticles with Pulmonary Surfactant.

SCIENCE CHINA Materials, 2015, 58, 28-37. (Q1)

[18] Meng Cao, Ziqi Ye, Xubo Lin, Ning Gu*. Advances in missing-in-metastasis research. Chinese Science

Bulletin, 2015, 60, 356-366. (In Chinese)

[19] Xubo Lin, Ning Gu*. Surface properties of encapsulating hydrophobic nanoparticles regulate the main phase

transition temperature of lipid bilayers: A simulation study. Nano Research, 2014, 7, 1195-1204. (Q1)

[20] Xubo Lin, Tingting Bai, Yi Y. Zuo, Ning Gu*. Promote Potential Applications of Nanoparticles as

Respiratory Drug Carrier: Insights from Molecular Dynamics Simulations. Nanoscale, 2014, 6, 2759-2767.

(Q1)

[21] Dandan Sun, Xubo Lin, Ning Gu*. Cholesterol Affects C60 Translocation across Lipid Bilayers. Soft Matter,

Curriculum Vitae - Xubo Lin

6/9

2014, 10, 2160-2168. (Q1)

[22] Ning Gu*, Xubo Lin. The Interactions of Medical Nanoparticles with Model Cell Membrane: A Review of

Simulation Studies. Progress in Biochemistry and Biophysics, 2013, 40, 918-924. (In Chinese)

[23] Xubo Lin, Changling Wang, Meng Wang, Kun Fang and Ning Gu*. Computer Simulation of the Effects of

Nanoparticles' Adsorption on the Properties of Supported Lipid Bilayer. Journal of Physical Chemistry C,

2012, 116, 17960-17968. (Q1)

[24] Xubo Lin, Yang Li and Ning Gu*. Molecular Dynamics Simulations of the Interactions of Charge-neutral

PAMAM Dendrimers with Pulmonary Surfactant. Soft Matter, 2011, 7, 3882-3888 (Selected by Virtual

Journal of Biological Physics Research, 2011, Volume 21, Issue 8; Reported by Obesity, Fitness and

Wellness Week and HighBeam Research) (Q1)

[25] Xubo Lin, Yang Li, and Ning Gu*. Nanoparticle’s Size Effect on Its Translocation across a Lipid Bilayer: A

Molecular Dynamics Simulation. Journal of Computational and Theoretical Nanoscience, 2010, 7, 269-276.

(Q2)

Book Chapters

[1] Yang Li, Xubo Lin, Ning Gu. Simulations on the Interactions of Nanomaterials with Cell Membrane. In Ning

Gu and Haiyan Xu, editors, The Interactions of Biomedical Nanomaterials with Cell. Chapter 8, pp. 246-285,

Science Press, 2014. (In Chinese)

[2] Dongfang Liu, Fei Xiong, Xubo Lin, Tingting Bai, Ning Gu. Surface Modification of Magnetic Nano-

Materials and Its Effects on Biomembrane. In Ning Gu, editor, Magnetic Nano-Materials and Devices for

Biomedical Applications. Chapter 6, pp. 139-164, Chemical Industry Press, 2013. (In Chinese, my figures are

selected as the cover figures.)

Others

Submitted:

[1] F. Tian, X. Lin*, R. P. Valle, Y. Zuo*, N. Gu*. PAMAM Dendrimer as a Respiratory Nanocarrier: Insights

from Experiments and Molecular Dynamics Simulations. Submitted.

Curriculum Vitae - Xubo Lin

7/9

CONFERENCES Invited Protein Workshop on Structure, Dynamics and Function at Beijing Computational Science

Research Center (CSRC), December 12-13, 2018, Beijing, China Oral 2018 Chinese Biomedical Engineering Annual Meeting (CBME2018), September 20-22, 2018,

Shenzhen, China. (In Chinese) Invited 过程工程所 60 周年系列活动之——“青年·逐梦·绿色·未来”学术研讨会暨过程工程

学术论坛，9 月 13 日，2018，中国 北京。

Attend 2018 Hangzhou Summit for Bio-innovatice Drug Preclinical Research & Clinical Application, September 8-9, 2018, Hangzhou, China.

Poster 16th Chinese Biophysics Congress, August 24-27, 2018, Chengdu, China. Oral Workshop “From Computational Biophysics to Systems Biology (CBSB2018)”, May 20-23, 2018,

Shenzhen, China. Invited The 1st International Symposium on Cell Bioinformatics, April 26-28, 2018, Nanjing, China Oral 2017 Medicine & Medicine-Engineering Zhizhen Recruiting Forum, June 16-18, 2017, Beijing,

China. (In Chinese) Oral Young Scientists’ Forum on Theoretical Physics and Interdisciplinary Studies (By Institute of

Theoretical Physics, Chinese Academy of Sciences), Jan. 12-14, 2017, Beijing, China. (In Chinese)Oral Beihang University Vision Forum for International Young Scholars, Dec. 16-19, 2016, Beijing,

China. (In Chinese) Attend Pittsburgh Supercomputing Center Anton2 Training Workshop (Invitation-only), Nov. 30, 2016,

Pittsburgh, Pennsylvania, USA. Poster CNLS 36th Annual Conference: Energy Landscapes: From Protein Folding to Molecular

Assembly, May 9-12, 2016, Santa Fe, New Mexico, USA. Poster Biophysical Society 60th Annual Meeting, Feb. 27- Mar. 2, 2016, Los Angeles, California, USA.Oral Workshop “From Computational Biophysics to Systems Biology (CBSB2015)”, May 17-19, 2015,

Oklahoma City, Oklahoma, USA. Poster 20th Annual Sealy Center for Structural Biology Symposium, May 2, 2015, Galveston, Texas,

USA. Poster The Fourth Symposium of the Chinese Protein Society 2013, Oct. 11-14, 2013, Hefei, China. (In

Chinese) Oral QUT-SEU Workshop on Nano Biotechnology, July 10-13, 2013, Nanjing, China. Poster The Fifth International Meeting on AFM in Life Sciences and Medicine, May 7-11, 2013,

Shanghai, China. Oral Doctoral Forum of Biological and Medical Nanotechnology (DFBMN 2012), July 10-13, 2012,

Suzhou. China. (In Chinese) Poster 17th International Biophysics Congress (IUPAB), Oct. 30 - Nov. 3, 2011, Beijing, China. Poster The International Conference on Computational and Systems Biology 2010 (iCCSB2010), Oct.

22-24, 2010, Hangzhou, China.

PROFESSIONAL SERVICES

Early Career Member of Chinese Society of Biomedical Engineering (2018~)

Early Career Member of Biophysical Society of China (2018~)

Early Career Member of American Chemical Society (2016~2017).

Curriculum Vitae - Xubo Lin

8/9

Early Career Member of American Biophysical Society (2015~2017).

Student Member of Chinese Biophysical Society (2011-2014).

Serve as a Committee Member for Mr. Yang Wang’s Ph.D. thesis defense @CSRC, Beijing, China.

Serve as the independent reviewer in peer-reviewing 6 scientific manuscripts for PLOS Computational Biology

(1), Colloids and Surfaces B: Biointerfaces (1), Current Topics in Medicinal Chemistry (2), PloS One (1),

Chinese Physics Letters (1).

Serve as the independent scientific reviewer for Cy-Tera and Eastern Mediterranean HPC proposal with Dr.

Stelios Erotokritou as the program coordinator (Proposal name: MOF design for efficient and safe drug

delivery), May 2016, Cyprus.

Participated in peer-reviewing 25 scientific manuscripts for Journal of the American Chemical Society (2),

ACS Nano (2), Journal of Physical Chemistry Letters (2), Small (1), Nanoscale (2), Soft Matter (2), Biophysical

Journal (5), Journal of Chemical Theory and Computation (1), PLOS Computational Biology (1), Journal of

Physical Chemistry B (3), Physical Chemistry Chemical Physics (1), Langmuir (1), Colloids and Surfaces B-

Biointerfaces (1), Frontiers of Physics (1).

Serve as the Co-secretary with Ms. Xiao Meng for QUT-SEU Workshop on Nano Biotechnology, July 10-13,

2013, Nanjing, China.

Serve as Poster Judge for 2015 Medical School Research Retreat, The University of Texas Health Science

Center at Houston.

TEACHING ACTIVITIES

Mentoring 2018/11~now Mentor my first undergraduate student, Fanzhe Meng, on PD-L1 modeling.

2018/10~now Mentor my first visiting graduate student, Shiying Zhou, on studying effects of food additives on lipid membranes.

2018/09~now Mentor my first full-time junior research assistant, Fujia Tian, on lipid nanobubble modeling.

2018/09~now Mentor my first graduate student, Xiaoqian Lin, on designing membrane-targeting nanoparticle.

12/2016~03/2017 Assist Prof. Alemayehu Gorfe mentoring a rotation PhD student, Vinay Nair, on transmembrane potential modelling. (Vinay co-authored a paper in Physical Chemistry Chemical Physics.)

10/2013-09/2014 Assist Prof. Ning Gu mentoring a master student, Zuoheng Zhang’s molecular dynamics simulation projects on nanoparticle-membrane interactions, Southeast University, Nanjing, China. (Zhang published his first paper in Colloids and Surfaces B: Biointerfaces.)

09/2012-09/2014 Assist Prof. Ning Gu mentoring a master student, Dandan Sun’s molecular dynamics simulation projects on C60-membrane & lipid nanobubble-membrane interactions, Southeast University, Nanjing, China. (Sun published her first paper in Soft Matter and second paper in Journal of Physical Chemistry C.)

Curriculum Vitae - Xubo Lin

9/9

03/2013-06/2013 Help a graduate student, Ying Sun with her molecular dynamics simulations on graphene-albumin interactions. (Sun publish her paper in Journal of Southeast University (Natural Science Edition))

10/2010-06/2011 Assist Prof. Ning Gu mentoring an undergraduate student, Yunzhao Ma’s graduation design projects. (Ma won Outstanding Graduate Design Team Award of Jiangsu province, Rank #2)

Updated by 01/28/2019