News & Highlights

IACS Travel Scholarship awarded to Chuan Tian

Congratulations! Chuan

New publication alert from Dr. He (Agnes) Huang

Congratulations to Agnes on her first-author JCTC article! While in the Simmerling Lab, Agnes worked on a faster implementation of calculating the Solvent Accessible Surface Area for biomolecules simulated in an implicit solvent. She leveraged the numerous cores on the GPU to increase the speed of her algorithm. Check out Agnes new paper below and look out for this new code in Amber19. Soon you can be estimating the non-polar contribution in your simulations without a noticeable slow down in your implicit solvent calculations.

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Simmerling Lab at the BNL GPU Hackathon

Members of the Simmerling Lab took part in a week-long GPU Hackathon hosted by Brookhaven National Lab on 17th to the 21st of September. The team consisted of Zach Fallon, Lauren Raugette, Kellon Belfon, and Chuan Tian. The goal of the team was to port the Center of Mass (CoM) Angle and Dihedral code into Amber18 PMEMD and PMEMD.cuda. Dr. Kevin Hauser, a past student in the lab was also instrumental in the team success by writing the CUDA kernels necessary for the CoM calculations. The team was successful in getting the CoM code working with the help of the mentors at the hackathon, Dr. Daniel Tian (NVIDIA) and Dr. Li Tang (BNL).


Preparing for the Hackathon during one of the Lab's coding meeting.

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Working hard at the Hackathon. The team won the #nosleep award.

Chuan Tian at the 256th ACS National Meeting

One of the most rewarding parts of research is presenting your work to other scientists. Chuan Tian got the opportunity to present a poster at the 256th ACS National Meeting in Boston. The title of his poster was "FF18SB: Improving the accuracy of Biomolecular Simulations". Look out for more information on this new forcefield. Outstanding work Chuan!

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Congratulations Dr. Angela Migues!

Dr. Angela Migues, a post-doc in our lab received a new position at SUNY Oneonta. She was helpful with the forcefield project and her research involved understanding replication fidelity in DNA Polymerase. All the best in your new position, we know you will do an excellent job.

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Angela last words to the lab:

"Don't be afraid to make mistakes, I have learned far more from my failures than my success"

2018 Sigma Xi Travel Award

Congratulations to Chuan Tian on your Sigma Xi Travel Award (2018).

We have a new Doctor in the house

Congratulations to Dr. Huang He 黄鹤 (Agnes) on successfully defending her thesis. During her PhD, Agnes created a faster method to calculate the non-polar solvation energy for MD simulation. She achieved this by leveraging the parallel architecture of GPUs. Look out for Agnes new code in Amber 18.

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Lauren Raguette awarded the best Teaching Assistant by Chemistry department

Congratulations Lauren on your Chemistry Award for First-Year Graduate Student Teaching Assistant. It is an honor to be awarded for your ability to make a tangible change in the education of the Undergraduates in the Chemistry department.

Ruth L. Kirschstein Predoctoral Individual National Research Service Award

Kellon's NRSA F31 application was selected for funding by the National Institute of General Medical Sciences. This award provides predoctoral individuals with supervised research training in specified health and health-related areas leading toward the research doctoral degree.

New Student Seungyoun Shin

Welcome, Seungyoun Shin to the Simmerling lab! Seungyoun is joining us from St. Edward's University.

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New Student Lauren Raguette

Welcome Lauren Raguette to the Simmerling lab! Lauren is joining us from Villanova University.

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ACM-SIGHPC/Intel Data Science Fellowship Award

Congratulations to Kellon Belfon for winning the prestigious Association of Computing Machinery (ACM) Special Interest Group on High-Performance Computing (SIGHPC)/Intel Computational Science and Data Science Fellowship!

Kellon is one of only 12 recipients for this award worldwide. Awardees were chosen based on their overall potential for excellence in data science and/or computational science, and the extent to which they will serve as leaders and role models to increase diversity in the workplace.

He was featured in SBU happening below

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Regeneron Science Talent Search

Annie Chang, a high school student from the Simmerling lab, was selected as one of the top 300 scholars in the prestigious national Regeneron Science Talent Search. Annie's project involved understanding the different effect that strong and weak inhibitors have on the dynamics of HIV protease's flaps. For her achievement, she was awarded $2000, a one-year subscription to Science News, and a certificate. Congratulations Annie

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2016 7th Annual CFN Image Challenge Winner

Congratulation Chuan Tian on being the winner of Brookhaven National Lab CFN image competition.

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Here is the announcement

New Student Zachary Fallon

Welcome, Zachary Fallon to the Simmerling lab! Zach is joining us from Adelphi University.

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New publication alert from Haoquan Li

"Congratulations to Haoquan for his first-author JACS article! Even though he has gone on to other things since being in our group, he did a really impressive job at continuing to move this project forward and finish another really strong paper." - Prof. Simmerling

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"Here, we use molecular dynamics simulations to explore the mechanism by which OGG1 discriminates between 8-oxoG and guanine along the base eversion pathway. MD results suggest an important role for kinking of the DNA by the glycosylase, which positions DNA phosphates in a way that assists lesion recognition during base eversion. The computational predictions were validated through experimental enzyme assays on phosphorothioate substrate analogs. Our simulations suggest that OGG1 distinguishes between 8-oxoG and G using their chemical dissimilarities not only at the active site, but also at earlier stages during base eversion, and this mechanism is at least partially conserved in Fpg despite lack of structural homology. The similarity also suggests that lesion recognition through multiple gating steps may be a common theme in DNA repair. Our results provide new insight into how enzymes can exploit kinetics and DNA conformational changes to probe the chemical modifications present in DNA lesions." - excerpt from the Abstract.

Check out the paper below

DNA deformation-coupled recognition of 8-oxoguanine: conformational kinetic gating in human DNA glycosylase.
Li, Haoquan; Endutkin, Anton; Bergonzo, Christina; Lin, Fu; Grollman, Arthur P.; Zharkov, Dmitry O.; Simmerling, Carlos, Journal of the American Chemical Society, 2016 accepted

A new doctor in the house [Kevin Hauser]

Dr. Kevin Hauser defended his thesis with an exciting talk that shed light on how a transcription factor, MTERF, search and recognize a specific sequence on DNA. His research focused on developing a model of protein-DNA search and recognition which described a sliding mechanism of MTERF on DNA.

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There is always time to celebrate after a great defense talk!

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Siemens Science competition semi-finalists

The Siemens Science Competition semi-finalists list is out [1] and Annie Chang is on it. Annie is a high school student that participated in the Siemens Science Research Program at SBU, this summer. She performed research in the Simmerling lab on understanding the effect of various drugs on HIV-1 PR flap dynamics. Congratulations on making it to the semi-finals.

New publication from Junjie Zou

Junjie Zou, a graduate student in the Simmerling and Raleigh lab, published his first paper in the lab. Outstanding job Junjie, congratulations!


Experimental and Computational Analysis of Protein Stabilization by Gly-to-D-Ala Substitution: A Convolution of Native State and Unfolded State Effects
Zou, Junjie; Song, Benben; Simmerling, Carlos; Raleigh, Daniel, Journal of the American Chemical Society, 2016 accepted

Congratulations Kevin Hauser!

Kevin Hauser started a post-doctoral position at Schrödinger. All the best Kevin, we know you will shine in your new position.

Congratulations Professor Simmerling!

Professor Carlos Simmerling was selected to the 2016 class of ACS Fellows, an elite group of 57 distinguished scientists who have made outstanding achievements in chemistry and contributed to the profession, science and ACS organization. Professor Simmerling was recognized at a ceremony on August 22, during the 252nd National ACS Meeting and Exposition in Philadelphia.

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Check out Professor Simmerling and the other 57 members of the 2016 class of ACS fellows:

Congratulations to Gabriela and Victoria!

Victoria and Gabriela (Undergraduates in the Simmerling lab) got accepted into the Ph.D. program at the University of Florida and the University of Pennsylvania respectively. All the best ladies in your future endeavors.

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Recently Published Manuscripts

Base flipping by MTERF1 can accommodate multiple conformations and occurs in a stepwise fashion
Byrnes, J.; Hauser, K.; Mejia, E.,; Norona, L.; Simmerling, C.; Garcia-Diaz, M.,J. Mol. Biol., 2016, 428 (12), 2542–2556

Advances in free-energy-based simulations of protein folding and ligand binding
Perez, A., Morrone, J. A., Simmerling, C., Dill, A.,Current opinion in structural biology 2016, 36, 25–31

A Dynamic Checkpoint in Oxidative Lesion Discrimination by Formamidopyrimidine–DNA Glycosylase
Li, H., Endutkin, A., Bergonzo, C., Grollman, A.; Campbell, A., de los Santos, C., Zharkov, D., Simmerling, C.,Nucleic Acids Research, 44 (2), 683–694

A human transcription factor in search mode
Hauser, K.; Essuman, B.; He, Y.; Coutsias, E.; Garcia-Diaz, M.; Simmerling, C., Nucleic Acids Research, 44 (1), 63–74

A grid-based backbone correction to the ff12SB protein force field for implicit-solvent simulations
Perez, A., MacCallum, JL., Brini, E., Simmerling, C., Dill, KA, J. Chem. Theor. Comput., 2015, 11 (10), 4770–4779
DOI: 10.1021/acs.jctc.5b00662