Aaron Santos

Aaron Santos
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Aaron Santos

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Pub Categories

Physics - Soft Condensed Matter (3)
Physics - Biological Physics (3)
Quantitative Biology - Biomolecules (2)
Physics - Other (1)
Physics - Mesoscopic Systems and Quantum Hall Effect (1)
Physics - Statistical Mechanics (1)
Physics - Computational Physics (1)

Publications Authored By Aaron Santos

We characterize the equation of state for a simple three-dimensional DNA hairpin model using a Metropolis Monte Carlo algorithm. This algorithm was run at constant temperature and fixed separation between the terminal ends of the strand. From the equation of state, we compute the compressibility, thermal expansion coefficient, and specific heat along with adiabatic path. Read More

We investigate kinetic pathways of the DNA melting transition using variable-range versions of the Poland-Scheraga (PS) and Peyrard-Dauxois-Bishop (PDB) models of DNA. In the PS model, we construct a phi^4-field theory to calculate the critical droplet profile, the initial growth modes, and the exponent characterizing the divergence of the susceptibility near the spinodal. In the PDB model, we use a mean field analysis to calculate susceptibility exponent. Read More

We present a microscopic theory that describes the ordering of two distinct ligands on the surface of a faceted nanoparticle. The theory predicts that when one type of ligand is significantly bulkier than all others, the larger ligands preferentially align themselves along the edges and vertices of the nanoparticle. Monte Carlo simulations confirm these predictions. Read More

We investigate the kinetics of the DNA melting transition using modified versions of the Peyrard-Dauxois-Bishop and Poland-Scheraga models that include long and short range interactions. Using Brownian dynamics and Monte Carlo simulations, we observe metastable states prior to nucleation and demonstrate that the profile and growth modes of the critical droplet can have both classical and spinodal characteristics depending on the interaction range and the temperature quench depth. Read More