Martín Carballo-Pacheco
I am currently a postdoctoral research scientist working with Dennis Vitkup at the Department of Systems Biology of Columbia University in New York City. I am interested on many aspects of biology, usually from a fundamental perspective, by applying concepts that lie in the interface of established research areas including computational chemistry, biophysics, molecular evolution, network theory and nonequilibrium physics.
Before, I was a postdoctoral research associate working with Rosalind Allen and Bartlomiej Waclaw at the School of Physics and Astronomy of the University of Edinburgh. I performed my PhD in Chemistry with Birgit Strodel and Ahmed E. Ismail at the AICES institute from RWTH Aachen University and at the Institute of Complex Systems 6: Structural Biochemistry from the Research Center Jülich. Even before, I did a Bachelor in Chemical Engineering working with Miguel Ladero Galán at the Chemistry Department of the Complutense University of Madrid and even before that I grew up in the very south of Argentina.
Research
Cancer Metabolism
Cancer cells are known to alter their cellular metabolism compared to normal cells. For example, the so-called "Warburg effect" means that cancer cells favor glycolysis instead of oxidative phosphorylation even though the second one is more efficient and preferred by most cells. We use genome scale metabolic models to understand the changes in metabolism in cancer cells.
The physics of antimicrobial resistance
The evolution of resistance to antibiotics by bacteria is one of the most urgent problems in healthcare. It also is a testbed for our understanding of molecular evolution. We use theoretical and computational models to understand different aspects of the emergence of antimicrobial resistance, including the effect of spatial heterogeneity and the effect of protein-antibiotic binding.
Functional and aberrant amyloids
Amyloids are highly structured protein aggregates usually associated with diseases such Alzheimer's, Parkinson's and type II diabetes. Recently, It was found that amyloids can also have physiologically normal roles. We investigate the aggregation of both functional and aberrant amyloids using molecular dynamics simulations, relating our results to experiments.
Method development: Simulating membranes implicitly
Membrane proteins account for 25% of eukaryotic proteins and 50% of drug targets. Simulating them can provide insight into their dynamics and folding. We developed a fast implicit solvent that can be used to accurately model membrane proteins.
Publications
10. M. Carballo-Pacheco*, M.D. Nicholson*, E.E. Lilja, R.J. Allen, B. Waclaw,
Phenotypic delay in the evolution of bacterial antibiotic resistance: mechanistic models and their implications,
bioRxiv 2019.12.19.883132 *shared first authors
9. P. Sinclair, M. Carballo-Pacheco, R.J. Allen,
Growth-dependent drug susceptibility can prevent or enhance spatial expansion of a bacterial population,
Physical Biology 16, 046001 (2019).
8. U. Sengupta, M. Carballo-Pacheco, B. Strodel,
Automated Markov state models for molecular dynamics simulations of aggregation and self-assembly,
Journal of Chemical Physics 150, 115101 (2019).
7. M. Carballo-Pacheco*, J. Desponds*, T. Gavrilchenko*, A. Mayer*, R. Prizak*, G. Reddy*, I. Nemenman, T. Mora,
Receptor crosstalk improves concentration sensing of multiple ligands,
Physical Review E 99, 022423 (2019). *shared first authors
6. M. Carballo-Pacheco, A.E. Ismail, B. Strodel,
On the applicability of force fields to study the aggregation of amyloidogenic peptides using molecular dynamics simulations,
Journal of Chemical Theory and Computation 14, 6063-6075 (2018).
5. M. Hora, M. Carballo-Pacheco, B. Weber, V. Morris, A. Wittkopf, J. Buchner, B. Strodel, B. Reif,
Epigallocatechin-3-gallate preferentially induces aggregation of amyloidogenic immunoglobulin light chains,
Scientific Reports 7, 41515 (2017).
4. M. Carballo-Pacheco, B. Strodel,
Comparison of force fields for Alzheimer’s Aβ42: A case study for intrinsically disordered proteins,
Protein Science 26, 174-185 (2017).
3. M. Carballo-Pacheco, B. Strodel,
Advances in the simulation of protein aggregation at the atomistic scale,
The Journal of Physical Chemistry B 120, 2991-2999 (2016).
Selected as part of the virtual issue "B is for Biophysics"
2. M. Carballo-Pacheco , A.E. Ismail, B. Strodel,
Oligomer formation of toxic and functional amyloid peptides studied with atomistic simulations,
The Journal of Physical Chemistry B 119, 9696-9705 (2015).
1. M. Carballo-Pacheco, I. Vancea, B. Strodel,
Extension of the FACTS implicit solvation model to membranes,
Journal of Chemical Theory and Computation 10, 3163-3176 (2014).
Some links
You can also check my work out in Researchgate and Google Scholar. Follow me on Twitter. (The picture up top is of the town of Killin and Loch Tay, a couple of hours away from Edinburgh in Scotland on a very snowy day)
Contact
mc4880 at