QLS-CMSP Joint seminar (Sergio Pantano) on 13 June 2022 at 11:00 CET

[Quantitative Life Sciences]

Dear All,

On Monday, 13 June at 11:00 CET, in the Central area, 2nd floor, old 
SISSA building, Via Beirut, 2

  Sergio Pantano (Institut Pasteur de Montevideo, Uruguay) will give a 
seminar titled:

*******************A coarse-grained approach to get viruses into your 
desktop computer: A close look into Zika virus structure and dynamics*


Abstract:

Physical Virology is a relatively new discipline aimed to unravel the 
physical forces that rule the assembly and destabilization of viral 
particles. Computational approaches can provide structural and dynamical 
insights into those processes. However, the computational cost of 
simulating entire viral particles constituted by millions of atoms is 
prohibitive without the use of supercomputer resources. We have 
developed a plug&play coarse-grained force field for biomolecules 
including topologies and interaction parameters for proteins, lipids, 
nucleic acids and aqueous solvent named SIRAH (Southamerican Initiative 
for a Rapid and Accurate Hamiltonian). Our force field grants over 2 
orders of magnitude speed up, making the simulation of viruses 
affordable to desktop computers.

We used this force field to characterize the dynamics of Zika virus, 
revealing unforeseen protein-lipid interactions that contribute to store 
significant tensile energy in the viral membrane, proposing it as an 
important factor in the spring-loaded configuration of the mature virion.

*References*

[1] Soñora M, Martínez L, Pantano S, Machado MR, Wrapping Up Viruses at 
Multiscale Resolution: Optimizing PACKMOL and SIRAH Execution for 
Simulating the Zika Virus. JCIM, 2021, 61:408

[2] Machado M, Gonzalez HC, Pantano S. MD Simulations of Virus-Like 
Particles with Supra CG solvation affordable to desktop computers. JCTC. 
2017, 13: 5106.

[3] Soñora M, Barrera EE, Zonta F, Pantano S, The stressed life of a 
lipid in the Zika Virus membrane, BBA – Membranes, 2022, 1864 (1), 183804.

/
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Indico page: https://indico.ictp.it/event/9979/


<https://zoom.us/j/475819702>


Best regards,

Erica


-- 
Erica Sarnataro
Group Secretary
Quantitative Life Sciences
The Abdus Salam International Centre for Theoretical Physics (ICTP)
Trieste,  Italy
Tel. +39-040-2240623
www.ictp.it/research/qls.aspx
e-mail:qls at ictp.it