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Dec 13, 2023
Our warmest congratulations to the newly minted Dr. Yumeng Zhang!
Yumeng successfully defended her PhD dissertation titled
"Multi-scale Simulations of Dynamic Protein Structures and
Interactions". She will join Prof. Bing Zhang's lab in MIT as a
postdoctoral fellow in Feburary 2024. Yumeng has made several
important contributions to the development of advanced methods for
more efficient and more accurate simulation of proteins. She has
also collaborated with experimentalists to exploit computer
simulation to obtain novel insights into the structure, dynamics and
interaction of functional proteins. She is a true role model and we
are going to deeply miss having her around the lab. Thankfully, we
do not need to say goodbye in another month or so ...
Dec 08, 2023
We are very prould to publish our 100th paper, in the prestigeous JACS no less!
In this article, we show that the HyRes coarse-grained protein model provides
a powerful tool to study the roles of protein backbone interaction and residual
structures in biomolecular phase separation. This is our first venture into the
exciting field of biomolecular condensates.
We are also very pleased to publish our BK predictor, where we show that physics
can help to overcome data scarcity problem in training machine learning models.
Key predictions were confirmed by new experiments!
In yet another exciting article, we show that hydrophobic gating and the canonical
helx bundle-crossing can work synergetically in ion channels!
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Dec 01, 2023
We are very thrilled to receive a new 5-year NIH R01 grant from NIA! We will
collaborate with PI Angsar Siemer's lab at USC and combine experiment and simulation
to study the roles of instrinsically disordered tails in controling alpha-synuclein
fibril structure and interaction!
Aug 29, 2023
Congratulations to Yumeng, Jian, Kairong, David and Shrishti for
highly successful presentations at the annual Chemistry ResearchFest
event. They were able to showcase several exciting projects from our
lab. Mahdieh came back as a Career Panelist and shared many valuable
wisdoms with the current graduate students. A special recognition
goes to Yumeng for being selected to give a coveted talk and winning
the prestigious Dr. Paul Hatheway Terry Endowment Award!
July 28 & Aug 26, 2023
Congratulations to Sam for successfully defending her Master thesis
titled "Combining Simulation and the MspA Nanopore to Study p53
Dynamics and Interactions"! During her time in the lab, Sam has made
several important contributions on simulation of nanopore hyration,
understanding how phosphorylation modulates dynamic interactions of
the disordered N-terminal domain of p53 with its DNA binding domain,
and devoloping nanopore-based approach for probing the structure and
intractions of disordered proteins such as p53. It is no joke that
Sam effectively defended a pseudo-PhD thesis for her Master degree
in Molecular and Ceullar Biology (MCB)!
The group (and friends and alums!) later celebrated Sam's
impressive two years in the Chens' labs and said good-bye at Jianhan's
house. We also discovered that our lab is full of great chefs!!!
July 21, 2023
Congatulations to the newly minted Dr. Gong! Xiping successfully defended
his PhD thesis titled "Atomistic simulations of intrinsically disordered
protein folding and dynamics". Xiping will move to University of Georgia
as a Research Scientist. He has been the technical guru of the lab and is going
to be dearly missed! It is very regretable that we did not get to have a
proper celebration party because Xiping and his family had to move earlier
than planned. Nonetheless, we had a little celebration in the lab and wished
Xiping and his family the best in Atlanta!
June 6, 2023
Mohit Yadav, a senior PhD student in CICS, joined the lab as a summer GRA.
Mohit will help to mentor Shrishti in the development of generative models
for dynamic protein conformations.
June 6, 2023
Congatulations to the newly minted Dr. Nordquist! Erik successfully defended
his PhD thesis titled "Understanding Protein Structure-Function Relationships
Using Simulations and Machine Learning". Erik will move to University of Maryland
as an NIH T32 Postdoctoral Fellow in Alex MacKerell's lab. He is going to be dearly
missed! The lab, family and friends got together at Jianhan's house and had
memorable celebration of Erik's highly accomplished five years at UMass. We
all wish him and Zoe the best in Baltimore!
May 16, 2023
We welcome back Juni Campbell as a Research Assistant before she joins our
Chemistry PhD program as a graduate student!
May 9, 2023
Congratulations to Shrishti for having her paper at UMass published in
Molecules. She co-first authored the review on
generative modeling of dynamic protein confirmations. We hope that
you will find it a great read!
April 1, 2023
This is no April fool's day joke! We are thrilled to welcome two new
PhD students from our MCB graduate program to the lab. Kairong Dong
came from one of the oldest cities in China, Xingtai of Hebei
province. She received her BS in Biotechnology from Central China
Normal University and MS in Biophysics from Chinese Academy of
Sciences, studying structure and mechanism of viral helicase-primase
D5. David DoCoeur came from Tallahassee, Florida. He received his BS
in Biochemistry from Florida State University with a minor in
biology. David was also a highly skilled appliance technician with
over 10 years experience. David will be a joint student with Min
Chen's lab, dedicating 100% to both computation and
experiment. Welcome to the lab, Kairong and David! We look forward
to having fun doing some great science together in the next few years!
March 10, 2023
After much delay, we were finally able to get together and celebrate
the Chinese (Lunar) New Year together! We are thankful for a great
year of Tiger and look forward to a prosperous year of Rabbit. We
welcomed Shanlong’s family, who were finally able to join him here,
and congratulated Erik for landing a great NIH T32 postdoc position
and Xiping and his wife for landing great faculty positions at UGA.
January 19, 2023
We had a simple lunch (pre)celebration of the Chinese New Year!
Wish everyone a super prosperous and heathy year of Bunny that is full of
joy, love and peace! We will have a real party when Shanlong's family
is here and everyone is back on campus. To be continued ...
December 18, 2022
We are thrilled that Shrishti Barthiya has officially joined the lab
as a Chemistry PhD student. Shrishti came from Gwalior, a
relatively small city in central India. She received an integrated
M.Sc. degree in Chemical Sciences from National Institute of Science
Education and Research (INSER) Bhubaneswar, working on machine
learning approaches for chemical dynamics simulations. In our lab,
Shrishti will explore new ways to combine molecular biophysics and
machine learning approaches for better description of complex
biological systems such as ion channels and intrinsically disordered
proteins. Welcome to the lab, Shrishti!
December 14, 2022
Our warmest congratulations to Jian for passing his ORP with an outstanding
performance! He is now officially a PhD candidate. We look forward to many
exciting research discoveries from Jian!
December 04, 2022
We welcome Dr. Shanlong Li to the lab as a postdoctoral fellow. Shanlong grew up in
Shandong, China and received his PhD in Polymer Chemistry and Physics from Shanghai
Jiao Tong University in China, under the direction of Profs. Yongfeng Zhou and Chunyang
Yu. His previous research focused on computer simulation of self-assembly processes and
computational design of nanoparticles. We look forward to many exciting directions that
we will be able to explore together at UMass!
November 18, 2022
We welcome Aron Korsunsky, a talented ChemE junior and tennis player, to our lab as
an undergraduate researcher!
November 1, 2022
Congratulations to Zhiguang for his co-first authored paper accepted by Nature
Communications! This is a collaborative work with Jianmin Cui's lab and focuses
on a novel agonist that mimics the calcium effects on the activation of
BK channels.
Also congratulations to Yumeng for having her beautiful HyResII model accepted
for publication in JCIM, to Sam (and Erik) her first paper on metadynamics studies
of nanopore hydration published in JPCB as a co-first author, and to Jian for his
first paper at UMass published in BJ as a co-first autor ...
August 30, 2022
Congratulations to Erik, Jian, Xiping and Yumeng for highly successful presentations
at the annual Chemistry ResearchFest event. They were able to showcase several exciting
projects from our lab. A special recognition goes to Erik for being selected to give
a coveted talk and winning the prestigious Dr. Paul Hatheway Terry Endowment Award!
July 26, 2022
Erik and Jianhan, together with Dr. Xueying Qin, organized and offered
an
Eureka! workshop on DNA extraction and Vitamin C content
measurement to a group of 10 8-grade girls. It was a lot of fun and
we were very pleased to see how these young scholars were awed and
inspired by (bio)chemistry!
June 6, 2022
Congratulations to Jian for receiving a competitive UMass CBI Traineeship.
Chemistry Biology Interface (CBI) is an NIH-funded
training program "to train students with diverse scientific backgrounds for productive
research at the interface between chemistry and biology" at UMass.
May 26, 2022
Our warmest congratulations to Zhiguang and his wife for welcoming their second son
to the world!
May 18, 2022
Congratulations to Ryan on wrapping up his highly accomplished career
at UMass. He will start graduate school in the Chemistry Department
at Boston University in the fall. We wish him the best luck!
Sam graduated with honor and a BS in Biochemistry ahead of schedule (in Fall 2021).
She will return as a fifth year Master student in MCB after a summer
intern in the industry.
We also welcome two new undergraduate interns this summer. Anik
Dey is a rising sophomore majoring in Biochemistry from Amherst
College and he will learn how to use computer to model and simulate
protein structure, dynamics and interaction. Jack Madden is a rising
sophomore majoring in computer science and pure math. He will work
on modernizing the Molecular
Playground in collaboration with Prof. Craig Martin.
May 1, 2022
Congratulations to Debabani, a former postdoc from the lab, on her
recent promotion to Associate Professor! We are so proud of you!
April 15, 2022
Congratulations to Erik for being selected as a 2022
CNS Teaching
Fellow. As a CNS Teaching Fellow, Erik will design a new seminar
course for the incoming first-year undergraduate students on a topic
of his choice. We all look forward to what amazing things Erik will
be able to do with this opportunity!
April 8, 2022
Congratulations to Jianhan for winning the 2022 CNS Outstanding Researh Award in
the Senior Faculty category! This award is really a recognition of the outstanding
dedication and collective achievements of our whole group!
Feburary 24, 2022
After 2 years of hiatus, the whole group (except Zhiguang) attended our first in-person
conference (BPS) in the beautiful San Francisco. We recruited perspective graduate students,
presented our works, learned about the latest progresses in the fields, and enjoyed
a bit of the city. Thanks to the snow storm, Erik, Xiping, Sam and Jian had to
take a rental car and drove back from Charlotte over two days. The consolation prize
was that they got to visit DC and NYC on their 800-mile way home!
January 29, 2022
Happy Chinese New Year! The lab and friends came together and celebrated another
challenging but rewarding year. We look forward to a prosperous New Year of Tiger!
January 11, 2022
We are thrilled to receive a 5-year MIRA grant from NIH/NIGMS to support continual
work on developing multi-scale methods for accurate simulation of disordered proteins
and dynamic interactions as well as the application of these methods to understand
a set of systems of significant biological and biomedical interests!
(UMass News Release)
December 13, 2021
Our warmest congratulations to Yumeng for passing her ORP and officially becoming
a PhD candidate!
November 26, 2021
We were thrilled to have Mahdieh and Xiaorong back visiting us during
the Thanksgiving break. Mahdieh and Xiaorong were able to make up (a
bit) for their lost opportunities to attend the graduation ceremony
due to the pandemic, by having our own mini hooding ceremony!
Congratulations on their achievements at UMass and we are so proud
of both of them! Mahdieh and Xiaorong were also able to share some
precious experience and wisdom on how to better prepare for
academic and industry careers.
November 10, 2021
A random beautiful day in New England. The group enjoyed the sunshine, ice cream,
and some great conversation together in front of LSL.
September 23, 2021
Congratulations to Erik for his first first-authored paper on DnaK modeling
accepted in principle by
PLoS Comp Biol!
Also congratulations to Xiping and Yumeng
for having their invited review article on multi-scale sampling/simulation of
IDPs accepted by Biomolecules!
September 18, 2021
The group celebrated the Mid-Autumn (Moon) Festival at Jianhan's house.
We finally got to welcome Jian and Samantha to the group in person, and had
some great muisc, food and games together.
August 3, 2021
After a whole year's delay, Jian Huang finally arrived from China.
A big shout-out to Erik and Xiping for taking the university van and
picking up Jian and three other fellow chemistry graduate students from
Boston. Welcome to Amherst, Jian! We are all thrilled to finally have
you here in person with us!
June 12, 2021
We had a joint group party with Min Chen's lab to celebrate summer as well as
our new NIAID award to develop the ClyA nanopore tweezers technology and study
flaviprotease dynamics and inhibition.
June 2, 2021
The group came together to celebrate all our blessings, including
summer, Zoe's new position at UMass, the international Children's
Day, conclusion of a long academic year, the official ending of
COVID restrictions, and many more! We also did a nice hike in Mount
Toby and explored the hidden wonder of Sunderland Cave!
May 6, 2021
Congratulations to Xiaorong for getting her work on p53 cancer mutations accepted
for publication in JMB. This is a very heavy paper that reflects a HUGE amount of
work from both simulation and experiment (with Drs. Zolkiewsi and Prakash from
Kansas State University) over the last 4 years. It is a very hard
project and we are very pleased that we now have something to show for
it.
April 6, 2021
Congratulations to Yumeng on passing the prospectus exam, the first milestone towards PhD!
Feburary 26, 2021
Our warmest congratulations to Mahdieh for landing a job of her dream! She is joining Merck
as a Senior Scientist as a member of their Computational and Structural Chemistry group.
We also offer our congratulations to former member Kuohao Lee, for his promotion to a
permanent Staff Scientist at NIH/NIDA. What a great way to kick start the Year of Ox!
Feburary 18, 2021
We warmly welcome Jian Huang as a new Ph.D. student to the lab! Jian came from Hengyang,
the "Wild Geese City" of China. He graduated first in his class with a B.S. in
Applied Chemistry from Huazhong University of Science and Technology in 2016. He then attended
the University of Chinese Academy of Sciences and obtained a M.S. in Biochemistry and
Molecular Biology in 2019, doing research in RNA biology under the direction of Jiangyun Wang
at the Institute of Biphysics of Chinese Academy of Sciences. We all look forward to
meeting Jian in person once he is able to get his visa and some exciting years working
together in computational biophysics!
Feburary 11, 2021
Happy Chinese New Year of Ox! We celebrated the new year together online and enjoyed
a few videos about the Chinese New Year traditions
and from the past CCTV Spring Festival Galas.
We wish everyone a great bull new year of great health, prosperity and happiness!
 
January 18, 2021
Happy New Year! The group had a modest celebration of the new year in the lab, while trying
our best to exercise good COVID-19 prevention practice. We also welcome two new undergraduate
researchers, Thomas and Samantha, to the lab! Both Tom and Samantha major in
biochemistry and molecular biology. We look forward to exploring some exciting new sciences
in the new year!
December 12, 2020
Congratulations to Zhiguang for getting his simulation on PIP2 activation of TMEM16A
channels accepted for publication in (Nature) Communication Biology! In this work,
we built on our collaborative work with Huanghe Yang's lab at Duke on the TMEM16
family protein activation and showed for the first time a likely activated state
of the TMEM16A channel.
December 11, 2020
Congratulations to Xiping and Erik for passing their Original Research Proposal (ORP) exams!
This is a major milestone. They are now both officially Ph.D. candidates!
December 08, 2020
Congratulations to Xiaorong for having her work on the interactions of anti-cancer
drug EGCG with p53 acccepted for publication in Nature Communications! This is
a collaborative work with Chunyu Wang at RPI and Stewart Loh at SUNY Upstate.
October 15, 2020
Fall is one of the most beautiful seasons in New England, besides Spring, Summer and Winter.
The group got together (after we all tested negative for COVID-19) and did a couple short hikes
along the famous Mohawk Trail.
The foliage was near peak and the weather was perfect! Thanks to an enthusiastic local,
we were very fortunate visit two of the most beautiful waterfalls in the area, as well as
allegedly the most haunted tunnel in New England (Hoosac Tunnel, East Portal). Check out
some of the pictures we took by clicking on the collage below. (Note: the tail to Twin
Cascades, pictur 18 below, starts next to Hoosac Tunnel, East Portal, picture 22 below)
August 29, 2020
After a small delay, the lab overcame COVID-19 and had a modest celebration of the newlyh minted
Dr. Yazdani in the lab! Congratulations!
August 25, 2020
Our warmest congratulations to Mahdieh for successfully defending her PhD dissertation!
Mahdieh gave an outstanding talk on her exciting discoveries on the regulation and gating
of BK channels. What a great ending to her celebrated tenure in our lab! It really speaks to
Mahdieh's outstanding dedication, perserverance and talent. COVID-19 was preventing us from
have a proper celebration, but not for too long ... Spring always comes!
August 18, 2020
Congratulations to Erik and Yumeng for winning the 2nd and 1st place prizes for their
poster presentations during the annual ResearchFest of UMass Chemistry!
August 13, 2020
Jianhan is joining the
Editorial Board of Biophysical Journal. The journal is published by
Cell Press on behalf of the Biophysical Society and a leading one on the physical studies
of a broad range of biological problems ranging from molecules to whole organisms.
August 13, 2020
We said good-bye to Xiaorong, mostly remotely. It was a very difficult, and bittersweet, moment.
Xiaorong has been a key member of our lab for the last several years, a true role model and
mentor to several younger graudate and undergraduate students She is an outstanding young
scientist and has made numerous contributions in multiple research areas. Well, all good
things must come to an end, for now. We wish Xiaorong and her family the best in Ann Arbor!
July 1, 2020
Congratulations to Erik for being selected for one of new CBI NIH Traineeships!
Chemistry Biology Interface (CBI) is an NIH-funded
training program "to train students with diverse scientific backgrounds for productive
research at the interface between chemistry and biology" at UMass.
June 28, 2020
Congratulations to Mahdieh and Zhiguang for getting their work on the role of so-called C-linker in
regulation and gating of BK channels accepted for publication in eLife! This is a
collaborative work with Jianmin Cui's lab at WUSTL. It is one of the first direct examples
of how nonspecific membrane interactions can modulate the channel function. It also suggests
that covalent linkages in membrane proteins should be considered an intergral component of
the sensing apparatus.
June 1, 2020
Congratulations to Mahdieh for passing her PhD data defense! There is no real hurdle between
Mahdieh and Dr ... Also congatulations to Xiping and Erik for reaching their first milestone
towards PhD, by passing the prospectus exam!
May 10, 2020
Congratulations to Xiaorong and her husband for their new baby son, born on the Mother's day!
Welcome to Earth, Zexi! We all look forward to meeeting you in person!
April 30, 2020
Our warm congratulations to Callie for being recognized with an ACS Undergraduate Award in Physical Chemistry!
April 27, 2020
After 6 weeks delay thanks to COVID-19, the group finally got together
for our spring outing. As a reward, we all got to visit our dream destinations! and yes, we do have some extreme
hardworkers who bring papers everywhere they go (including vacations) ...
March 16, 2020
Warmest congratulations to Zhiguang for getting his work on
multi-scale modeling of amyloid formation accepted for publication
in PNAS! This is a result of two years' hard work from Zhiguang. He
has developed a multi-scale approach that provides a complete
description of fibril growth at atomistic level for the first time
and can recaptitulate the sequence dependence of fibril growth
mechanism and kinetics without any free parameter!
Jan 19, 2020
The group celebrated the Chinese New Year together in Jianhan's
house and looked forward to a great Year of Rat!
Jan 1, 2020
Another new decade, another exciting chapter in the journey?!
路漫漫其修远兮，吾将上下而求索（屈原）
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