A5002466855- Genomics and Chromatin Dynamics
- Parasites and Host Interactions
- Helminth infection and control
- Machine Learning in Materials Science
- Advanced NMR Techniques and Applications
- Protein Structure and Dynamics
- Particle accelerators and beam dynamics
- Spectroscopy and Quantum Chemical Studies
- RNA Research and Splicing
- Epigenetics and DNA Methylation
- Research on Leishmaniasis Studies
- Quantum chaos and dynamical systems
- Theoretical and Computational Physics
- Advanced Chemical Physics Studies
- Plant Molecular Biology Research
- Parasite Biology and Host Interactions
- Genomic variations and chromosomal abnormalities
- Spectroscopy and Laser Applications
- Diffusion and Search Dynamics
- RNA and protein synthesis mechanisms
- Advanced Physical and Chemical Molecular Interactions
École Polytechnique Fédérale de Lausanne
2020-2024
University of Edinburgh
2016-2020
ConspectusFirst-principles molecular dynamics (FPMD) and its quantum mechanical-molecular mechanical (QM/MM) extensions are powerful tools to follow the real-time of a broad variety systems in their ground as well electronically excited states. The continued advances computational power have enabled simulations QM regions larger sizes for more extended time scales. In addition, development parallel algorithms has boosted performance QM/MM methods even on existing computer architectures. case...
MiMiC is a framework for performing multiscale simulations in which loosely coupled external programs describe individual subsystems at different resolutions and levels of theory. To make it highly efficient flexible, we adopt an interoperable approach based on multiple-program multiple-data (MPMD) paradigm, serving as intermediary responsible fast data exchange interactions between the subsystems. The main goal to avoid interfering with underlying parallelization programs, including...
MiMiC is a framework for performing multiscale simulations in which loosely coupled external programs describe individual subsystems at different resolutions and levels of theory. To make it highly efficient flexible, we adopt an interoperable approach based on multiple-program multiple-data (MPMD) paradigm, serving as intermediary responsible fast data exchange interactions between the subsystems. The main goal to avoid interfering with underlying parallelization programs, including...
Abstract Fluorescence microscopy reveals that the contents of many (membrane-free) nuclear “bodies” exchange rapidly with soluble pool whilst underlying structure persists; such observations await a satisfactory biophysical explanation. To shed light on this, we perform large-scale Brownian dynamics simulations chromatin fiber interacting an ensemble (multivalent) DNA-binding proteins; these proteins switch between two states – active (binding) and inactive (non-binding). This system...
We discuss a polymer model for the 3D organization of human chromosomes. A chromosome is represented by string beads, with each bead being "colored" according to 1D bioinformatic data (e.g., chromatin state, histone modification, GC content). Individual spheres (representing bi- and multi-valent transcription factors) can bind reversibly selectively beads appropriate color. During molecular dynamics simulations, factors bind, spontaneously folds into loops, rosettes,...
Abstract Schistosomiasis is a disease of poverty affecting millions people. Praziquantel (PZQ), with its strengths and weaknesses, the only treatment available. We previously reported findings on three lead compounds derived from oxamniquine (OXA), an old antischistosomal drug: ferrocene‐containing (Fc‐CH 2 ‐OXA), ruthenocene‐containing (Rc‐CH ‐OXA) benzene‐containing (Ph‐CH OXA derivatives. These derivatives showed excellent in vitro activity against both Schistosoma mansoni larvae adult...
A multiple time step (MTS) algorithm for trajectory surface hopping molecular dynamics has been developed, implemented, and tested. The MTS scheme is an extension of the ab initio implementation Born-Oppenheimer presented in work Liberatore et al. [J. Chem. Theory Comput. 14, 2834 (2018)]. In particular, modified to enable simulation non-adiabatic processes with (TSH) method Tully's fewest switches algorithm. specificities lie combination Landau-Zener transition probabilities during inner...
We discuss a polymer model for the 3D organization of human chromosomes. A chromosome is represented by string beads, with each bead being "colored" according to 1D bioinformatic data (e.g., chromatin state, histone modification, GC content). Individual spheres (representing bi- and multi-valent transcription factors) can bind reversibly selectively beads appropriate color. During molecular dynamics simulations, factors bind, spontaneously folds into loops, rosettes,...
Schistosomiasis is a disease of poverty affecting millions people. Praziquantel (PZQ), with its strengths and weaknesses, the only treatment available. We previously reported 3 lead compounds derived from oxamniquine (OXA), an old antischistosomal drug: ferrocene‐containing (Fc‐CH2‐OXA), ruthenocene‐containing (Rc‐CH2‐OXA) benzene‐containing (Ph‐CH2‐OXA). These derivatives showed excellent in vitro activity against both Schistosoma mansoni S. haematobium larvae adult worms, vivo mansoni....
<div>Schistosomiasis is a disease of poverty affecting millions people. Praziquantel (PZQ), with its </div><div>strengths and weaknesses, the only treatment available. We previously reported 3 lead </div><div>compounds derived from oxamniquine (OXA), an old antischistosomal drug: ferrocene‐containing </div><div>(Fc‐CH2‐OXA), ruthenocene‐containing (Rc‐CH2‐OXA) benzene‐containing (Ph‐CH2‐OXA). </div><div>These derivatives showed excellent...