By quenching into the metastable region of the three-dimensional Ising model, we investigate the paths that the magnetization (energy) takes as a function of time. We accumulate the magnetization (energy) paths into time-dependent distributions from which we reconstruct the free energy as a function of the magnetic field, temperature, and system size. From the reconstructed free energy, we obta...

Abstract. In this paper, a predator-prey-disease model with immune response in the infected prey is formulated. The basic reproduction number of the within-host model is defined and it is found that there are three equilibria: extinction equilibrium, infection-free equilibrium and infection-persistent equilibrium. The stabilities of these equilibria are completely determined by the reproduction...

Introduction: Fully refocused steady-state free precession (SSFP) is a fast imaging sequence offering high SNR efficiency. Extensions to SSFP such as fluctuating equilibrium [l] and linear combination SSFP [2] enable water-fat separation and immunity to off-resonance. Because of the volatile transient response during the approach to steady state, data acquisition is usually delayed until this t...

Title of dissertation: Equilibrium free energies from nonequilibrium simulations: Improving convergence by reducing dissipation Suriyanarayanan Vaikuntanathan, Doctor of Philosophy, 2011 Dissertation directed by: Professor Christopher Jarzynski Department of Chemistry and Biochemistry Institute for Physical Science and Technology The estimation of equilibrium free energy differences is an impor...

A scheme for extracting an effective free energy landscape from single-molecule time series is presented. This procedure uniquely identifies a non-Gaussian distribution of the observable associated with each local equilibrium state (LES). Both the number of LESs and the shape of the non-Gaussian distributions depend on the time scale of observation. By assessing how often the system visits and ...

What is the free energy source enabling high-fidelity DNA polymerases (pols) to favor incorporation of correct over incorrect base pairs by 10(3)- to 10(4)-fold, corresponding to free energy differences of ΔΔGinc∼ 5.5-7 kcal/mol? Standard ΔΔG° values (∼0.3 kcal/mol) calculated from melting temperature measurements comparing matched vs. mismatched base pairs at duplex DNA termini are far too low...

Hydride transfer changes the charge structure of the reactant and thus, may induce reorientation/reorganization of solvent molecules. This solvent reorganization may in turn alter the energetics of the reaction. In the present work, we investigate the intramolecular hydride transfer by taking Lewis acid catalyzed glucose to fructose isomerization as an example. The C2-C1 hydride transfer is the...