Correct calculation of the variation of free energy upon base flipping is crucial in understanding the dynamics of DNA systems. The free energy landscape along the flipping pathway gives the thermodynamic stability and the flexibility of base-paired states. Although numerous free energy simulations are performed in the base flipping cases, no theoretically rigorous nonequilibrium techniques are devised and employed to investigate the thermodynamics of base flipping. In the current work, we report a general nonequilibrium stratification scheme for the efficient calculation of the free energy landscape of base flipping in DNA duplex. We carefully monitor the convergence behavior of the equilibrium sampling based free energy simulation and the nonequilibrium stratification and determine the empirical length of time blocks required for converged sampling. Comparison between the performances of the equilibrium umbrella sampling and the nonequilibrium stratification is given. The results show that nonequilibrium free energy simulation achieves similar accuracy and efficiency compared with the equilibrium enhanced sampling technique in the base flipping cases. We further test a convergence criterion we previously proposed and it comes out that the convergence determined by this criterion agrees with those given by the time-invariant behavior of PMF and the nonlinear dependence of standard deviation on the sample size.2 / 41

Indocyanine green-platinum porphyrins integrated conjugated polymer hybrid nanoparticles for bimodal photothermal and two-photon photodynamic therapy with near-infrared irradiation.

In order to search for a suitable frequency and material with higher photothermal efficacy for hyperthermia application in cancer treatment, a comparative study on laser heating of Au/Ag nanoparticles and Ag nanowires has been conducted. It is found that gold nanoparticles are more photothermal efficient in comparison with silver nanoparticles and silver nanowires at 450nm and 532 nm. Gold nanoparticles are more heated by 532 nm laser than 450 nm laser. In contrast, silver nanoparticles show slightly less temperature rise at 532 nm than 450 nm laser. For silver nanowires, no significant photothermal effect has been observed. Size-dependent effect study indicates that the absorption efficiency of single gold nanoparticles of larger diameter is higher than that of smaller diameter, in the diameter range of 0-50nm. A mathematical model for describing the heating profile in the heating sample has been built. The mathematical model can be utilized to predict the optimal treatment size of tumor.

We have deployed a wireless network that operates in the white spaces of the TV band spectrum and covers most of Microsoft campus in Redmond, WA. Since the campus is large (approximately 1 mile x 1 mile), there are several shuttles that move employees from one building to another. We have used the white spaces network to enable a key productivity scenario on campus - Internet connectivity in campus shuttles. We have modified one such shuttle to operate over the TV band white spaces. A white space radio in this shuttle communicates with two base stations deployed on buildings on campus. Inside the shuttle, we bridge the white space connection to Wi-Fi, so that an employee's laptop that does not have an integrated white space radio can nevertheless connect to the Internet, using Wi-Fi within the shuttle, and white spaces between the shuttle and the base stations. To the best of our knowledge, this is the first network deployed over the TV white spaces.