LoverdeLab

Loverde Laboratory

Computational biophysics of chromatin and soft biological matter at the College of Staten Island and the CUNY Graduate Center.

Nucleosomes along a chromatin fiber, drawn in coarse-grained bead style. Histone cores: H3 teal, H4 pink, H2A gold, H2B orange.

Overview

We use all-atom and coarse-grained molecular dynamics to understand how biological assemblies hold together, move, and fall apart. Our central system is the nucleosome, the basic packaging unit of the genome. We ask how histone tails, DNA sequence, histone variants, and cancer-associated mutations change its dynamics, and how those changes are communicated across the structure. The same multiscale toolkit drives our work on peptide condensates and supramolecular materials for drug delivery.

Our simulations run on the CUNY High Performance Computing Center, NSF ACCESS, and the Anton 3 special-purpose supercomputer at the Pittsburgh Supercomputing Center. We work closely with experimental groups, and we release code and, where possible, trajectories with most of our papers.

Anton 3Long-timescale all-atom simulations of nucleosomes
Open scienceCode on GitHub and trajectories on Zenodo for most papers
CUNY trainingUndergraduates through PhD in Chemistry, Biochemistry, Physics

Research

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Recent news

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Join us

We welcome rotation students and prospective PhD students in Chemistry, Biochemistry, and Physics at the CUNY Graduate Center, as well as CSI undergraduates. No prior simulation experience is required.