Computational Biophysics @ UVM

Juan Vanegas, Ph.D.
Assistant Professor
Department of Physics
University of Vermont
Cook Physical Science Bldg. A521 - (802) 656-0049
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Faculty member of the UVM Materials Science and Cellular, Molecular, and Biomedical Sciences graduate programs.

Research Interests

We use coarse-grained, atomistic, and ab initio molecular simulation methods to understand the physical principles underlying the function of biological systems. Some applications of our research include lipid biomembranes, mechanosensitive channels, and enzymatic catalysis. We are also interested in understanding the connection between chemical structure and mechanical properties at the nanoscale. We have contributed to the development of local stress calculations from molecular dynamics simulation and its implementation in the GROMACS-LS and MDStress codes.

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Selected Publications

(Complete list)

Torres-Sanchez, A., Vanegas, J. M., and Arroyo, M. Geometric derivation of the microscopic stress: A covariant central force decomposition. J. Mech. Phys. Solids 93, 224 – 239 (2016) [PDF]
Abstract. We revisit the derivation of the microscopic stress, linking the statistical mechanics of particle systems and continuum mechanics. The starting point in our geometric derivation is the Doyle–Ericksen formula [...]

Torres-Sanchez, A., Vanegas, J. M., and Arroyo, M. Examining the mechanical equilibrium of microscopic stresses in molecular simulations. Phys. Rev. Lett. 114, 258102 (2015). [PDF]
Abstract. The microscopic stress field provides a unique connection between atomistic simulations and mechanics at the nanoscale. However, its definition remains ambiguous. Rather than a mere theoretical [...]

Anishkin, A., Vanegas, J. M., Rogers, D. M., Lorenzi, P. L., Chan, W. K., Purwaha, P., Weinstein, J. N., Sukharev, S., and Rempe, S. B. Catalytic role of the substrate defines specificity of therapeutic L-asparaginase. J. Mol. Biol. 427, (17), 2867–2885 (2015) [PDF]
Abstract. Type II bacterial l-asparaginases (l-ASP) have played an important therapeutic role in cancer treatment for over four decades, yet their exact [...]

Vanegas, J. M. and Arroyo, M. Force transduction and lipid binding in MscL: A continuum-molecular approach. PLoS ONE, 9 (12), e113947. (2014) [PDF]
Abstract. The bacterial mechanosensitive channel MscL, a small protein mainly activated by membrane tension, is a central model system to study the transduction of mechanical stimuli into chemical signals. Mutagenic studies suggest that MscL gating strongly depends on both intra-protein and interfacial lipid-protein interactions. However, there is a gap between this [...]

Vanegas, J. M., Torres-Sanchez, A., and Arroyo, M. Importance of force decomposition for local stress calculations in biomembrane molecular simulations. J. Chem. Theory Comput., 10, 691-702. (2014) [PDF]
Abstract. Local stress fields are routinely computed from molecular dynamics trajectories to understand the structure and mechanical properties of lipid bilayers. These calculations can be systematically understood with the Irving–Kirkwood–Noll theory. In identifying the stress tensor, a crucial step is the decomposition of the forces on the particles into pairwise [...]