2023 February: Thank you Biophysical Society!
The entire lab is excited to participate and present our research at the2023 Biophysical Society meeting. Mohd Ahsan, post-doc in the lab, receives the post-doctoral travel award. Giulia receives the Theory and Computation Subgroup Early Career Award.
2022 October: NERSC Honors Early Career Researchers with 2022 Achievement Awards
Our lab receives the Innovative Use of High Performance Computing award from the National Energy Research Scientific Computing Center – NERSC. This award recognized four early-career scientists who have made significant contributions to scientific computation using NERSC resources.
2022 May: Outstanding Doctoral Dissertation Advisor/Mentoring Award
Giulia receives the Outstanding Doctoral Dissertation Advisor/Mentoring Award from UCR. Our lab is striving to create new educational programs to mentor and encourage young students, including underrepresented minorities and women. We are very honored and humbled to receive this recognition, which further inspires our lab to excel in education.
2022 March: ACS OpenEye Outstanding Junior Faculty Award
Giulia receives the ACS OpenEye Outstanding Junior Faculty Award
2022 January: NSF CAREER award
We are grateful to the National Science Foundation for awarding us the NSF CAREER award! This will give us the opportunity to pursue exciting research and high-level education to mentor undergraduate and K12 students, including underrepresented minorities and women.
2021 September: JACS features our paper in the 2021 Early Career Investigators Virtual Issue
JACS has featured our paper in the 2021 Early Career Investigators Virtual Issue! This is the second time that JACS recognizes our work in this prestigious special issue. Our paper in JACS on the PAM-mediated allostery in Cas9 was selected for the 2018 Early Career Edition! Congratulations to all authors!
“This work demonstrates the tremendous value of combined NMR and state-of-the-art molecular dynamics in characterizing allostery”
2021 September: Giulia receives the 2020 Corwin Hansch Award
This award is given by the Hansch-Fujita Foundation to an outstanding scientist under the age of 40 for significant contributions to the field of computational drug design. The award is named in honor of Corwin Hansch, a pioneer in computational drug discovery and late honorary chair of the QSAR & Chemoinformatics Society.
2021 June: We Love Molecular Dynamics is out!
Our new website dedicated to our outreaching and educational activities is out! WeLoveMolecularDynamics was inspired by the passion that high school students and undergraduates expressed for computational biophysics. Visit the website to know more about our programs and to join us from high schools! We aim at mentoring young students, including underrepresented minorities and women, to engage in higher education.
2021 May: Pablo Arantes will give a talk at the CRISPR meeting
Congratulations to Pablo Arantes, who will present his work using molecular dynamics to understand the off-target interactions in CRISPR-Cas9 at the virtual CRISPR meeting!
2021 May: PSC highlights our research using Anton-2!
2021 February: Aakash Saha receives the Student Research Achievement Award from the BPS
Congratulations to Aakash Saha for receiving the Biophysical Society 2021 Student Research Achievement Award in the Bioengineering subgroup!
2021 January: Aakash Saha receives the outstanding Teaching Assistant award at UCR
Congratulations to Aakash for being such a fantastic scientist and teacher!
2020 December: Our first NERSC grant!
We are grateful to NERSC, which awards us computer time at the facilities of the Lawrence Berkeley National Lab to initiate a new project on genome editing technologies (grant m3807).
2020 November: Amun Patel joins our lab as a graduate student!
2020 October: Exciting Nobel Prize in Chemistry!
Our lab is excited for the 2020 Nobel Prize in Chemistry to Jennifer A. Doudna & Emmanuelle Charpentier for the development of new genome editing technologies.
2020 September: New grant from XSEDE!
The Extreme Science and Engineering Discovery Environment XSEDE awards us again! We are very grateful for the opportunity to continue running classical and ab-initio simulations on the XSEDE facilities (grant TG-MCB160059).
2020 May: The COVID19 HPC consortium grants us computer time on Anton-2!
We are thankful to the COVID-19 HPC consortium for awarding us computer time on Anton-2 to pursue research on the detection of SARS-CoV-2 using emerging CRISPR technologies!
2020 April: Special Issue on Multiscale Modeling from Macromolecules to Cell
Our Special Issue in Frontiers in Molecular Biosciences is finally out! We collected several papers at the frontier of molecular simulation techniques. This special issue ranks the second in the section “Computer modeling and simulation” (after a topic on Covid19) and is in the top 10% of the entire journal “Frontiers in molecular biosciences” with more than 70,000 views!
2020 February: The Morikis Memorial Symposium
Our lab is honoured to organise and participate to the Professor Morikis Memorial Symposium to honour the memory of our beloved mentor Prof. Dimitrios Morikis. Download here the Booklet of the symposium.
2019 September: NSF funds our research!
We are grateful to the National Science Foundation and to the Chemistry division for awarding us a research grant that will support our research and our educational program!
2019 August: Women Make COMP at the ACS meeting!
We are excited for the first Women Make COMP symposium at the ACS Meeting! Established women in computational chemistry are meeting young scientists to inspire the next generation of women in computational chemistry!
2019 June: Special issue on CryoEM modeling
2019 March: First XSEDE grant of the Palermo lab!
The Extreme Science and Engineering Discovery Environment XSEDE awards computer time to our lab to perform our research (grant TG-MCB160059).
2019 March: Biophysical Society meeting in Baltimore
Excited to be @BiophysicalSoc for
#BPS2019! Our lab gave a talk on the off-target effects in #CRISPR and a poster on its #allosteric regulation with great feedback! We are also honoured for being at the #Art&Science contest with our COVER ART!
2019 February: CECAM workshop on multiscale modeling!
Giulia co-organises the CECAM workshop at the Swiss Federal Institute of Technology in Lausanne on the next frontiers in musicale modeling. To highlight the state-of-the-art, to tackle the current challenges and to inspire future innovations! The outcomes of this workshop are featured in a Special Issue on Frontiers in Molecular Biosciences.
2018 Fall: Our lab is growing!
Brandon Mitchell and Nasim Farajpour join the lab as a graduate students, with Dominic Biondo who is currently rotating. Two undergraduate students have also joined the lab: Marco Medrano and Ponmathi Jayaseelan.
2018 August: COMP meets CRYO @ACS meeting.
Giulia co-organises the symposium “COMP meets CRYO: new frontiers in flexible fitting, image processing and refinement of cryo-EM data” at the 256th ACS meeting in Boston.
2018 July: CECAM workshop on modelling metal ions!
Giulia co-organises the CECAM workshop @ParisTech Frontiers and challenges of computing metals for biochemical, medical and technological applications.
2018 July: Official birthday of the Palermo lab!
The Palermo lab is up & running at the University of California Riverside. Our lab gets equipped with four Linux workstations, which include two GPUs (an Nvidia GTX-class for GPU computing and an Nvidia Quadro for interactive visualization) and 12 Intel Xeon cores. High Performance Computing is provided us thanks to the UCR HPCC and XSEDE (grant TG-MCB160059).
2018 June: we are on the cover!
Giulia becomes an Early Career Board member of the Journal of Chemical Information and Modelling.
It is a honour and a pleasure having been selected for the Early Career Board of the #JCIM_ACS. I am proud to be part of a team of brilliant young scientists for pushing the frontiers of computer simulations!
2018 February: The Biophysical Society features our research!
I am honored to be part to the prestigious symposium “Future of Biophysics” of the Biophysical Society, presenting our research on the mechanistic understanding of genome editing technologies. This has been an amazing experience with top scientists across the globe.
2017 November: Best use of HPC in Life Sciences!
I am happy to receive the 2017 HPC wire prize for Best use of High Performance Computing (HPC) in Life Science! This prize recognise the effort we have done over the years to bridge high-level theoretical chemistry with real-world biological sciences.
2017 August: Allosteric effects in CRISPR-Cas9!
By using molecular dynamics and network models derived from graph theory, we published in JACS the discovery of an allosteric mechanism in CRISPR-Cas9 that enables for DNA processing upon recognition! We are on the cover with the beautiful artwork of Dr. Clarisse G. Ricci!
2017 June: An other piece in the puzzle of CRISPR-Cas9
Our paper in PNAS highlighted in the San Diego Supercomputer Center news! Our supercluster ‘Comet’ helps break the “millisecond barrier” for complex biological simulations. Read how Gaussian accelerated Molecular Dynamics (GaMD) simulations helped in understanding the conformational activation of CRISPR-Cas9.
2017 March: Anticancer drug gets a boost with antirheumatic
Molecular dynamics and X-ray crystallography have discovered that combining an anticancer drug with an antirheumatic produces improved effects against tumors. Our paper in Nature Communications paves the way for novel strategies in anticancer drug discovery. Read our story on Science Daily and in French on 20min!
2017 February: First place prize at the Art & Science image contest!
We thank all members of the Biophysical Society for having awarded us the first place prize at the 2017 Biophysical Society national meeting in New Orleans! I am equally sharing this prize with my friends and colleagues Amelia Palermo (ETH-Zürich, handmade painting) and Lorenzo Casalino (SISSA-Trieste, digital manipulation).
2016 September: Supercomputers reveal acrobatics of CRISPR-Cas9
First simulations of CRISPR-Cas9 published in ACS Cent Sci. We predict the key role of the non-target DNA in the activation process with insights for structure-based engineering toward improved genome editing! Check it out in the news!
2016 June: Cover of the AMBER 16 manual!
AMBER is a simulation code and – more broadly – a school for rigorous molecular simulations. I feel excited for being on the cover of the AMBER 2016 reference manual with my painting of the “Steitz & Steitz” mechanism. This painting describes the role of metal ions in the enzymatic processing of DNA & RNA, which is a paradigm in biology, discovered in 1993 by Seitz & Seitz! We have published mechanistic investigations via theoretical methods in Acc Chem Res and in JCTC.
2016 June: The RNA that snips and stitches RNA
By using quantum/classical molecular simulations and the Car-Parrinello approach, our paper in JACS describes the mechanism of RNA cleavage, in self-splicing ribozymes! This paper poses the basis for understanding splicing in humans. Read our press release on Science Newsline Biology and Science Daily.
2015 December: Metal Drugs to Fight Cancer
Metal drugs are a challenge for molecular simulations. By using quantum-classical simulations, we revealed how novel metal drugs compounds interfere with chromatin compaction and post-translational modifications, being promising against cancer. Read our story on Science Daily.