Effective Dynamics for Stochastic Differential Equations

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Explores Generalized Langevin Equations and their computational implications in molecular dynamics simulations, emphasizing the impact of noise details on particle trajectories.

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Polymer Collapse: Covolume and Free Energy

Explores polymer collapse, emphasizing covolume and free energy in the process.

Nonequilibrium Free Energy Equality

Covers the nonequilibrium equality for free energy differences proposed by Crooks and Jarzynski in 1997.

Jarzynski Equation and Quantum Circuits

Explores the Jarzynski equation and the quantization of electrical circuits in quantum harmonic oscillators.

Molecular Dynamics and Monte Carlo

Covers computational methods for molecular systems at finite temperature, emphasizing stochastic sampling and time evolution simulations.

Molecular dynamics under constraints

Explores molecular dynamics simulations under holonomic constraints, focusing on numerical integration and algorithm formulation.

Thermodynamics: Entropy and Ideal Gases

Explores entropy, ideal gases, and TDS equations in thermodynamics, emphasizing the importance of the Clausius inequality and the Carnot cycle.

Entropy and Carnot Cycle

Covers entropy, Carnot cycle optimality, and free energy minimization in spontaneous processes.

Energy Minimization in Biological Systems: Equilibrium Models

Covers energy minimization models in biological systems, focusing on equilibrium and the roles of entropy and hydrophobicity.