Heating, equilibration protocols

After the initial configuration construction, we performed a standard equilibration protocol for DNA simulations [20]. The entire structure was minimized by the steepest descent method in order to avoid close atomic contacts, followed by slow constant volume heating to 300 K over 100 ps using 2.4 kcal/mol harmonic restraints. These restraints were slowly reduced to zero during a series of energy minimization and 50 ps equilibration steps at constant temperature (300 K) and pressure (1 bar) with a 0.2 ps coupling constant for both parameters. The final equilibration step was a 100 ps constant volume run. 

Failure to achieve the optimal temperature required for heat induced antigen retrieval. When using a waterbath or steamer, allow sufficient time for the retrieval buffer to equilibrate to a temperature range of 95-99 °C. At high altitude (greater than-4,500 feet), the buffer will boil at less than 95 °C. Utilize a closed heating system such as a pressure cooker, autoclave or Pascal, or utilize a low temperature protocol if standardization of the validated procedure is not affected. 51-65... 

Figure 4 Tentative MD protocol for simulating hydrated nucleic acid (NA) systems. (Tw) thermalization of the water molecules (Twi) conjugate thermalization of the ioas and the water molecules (H) heating of the entire system (E) equilibration of the system at 300 K (P) production phase. The length of these different steps is. obviously, highly dependent on available computational means...

On study days, sows received 11 meals equivalent to 1/26 of their daily ration every 30 minutes. Comparability of this protocol to once daily feeding and adequacy of the adaptation period was previously verified (Moehn etal, 2004). Sows were individually housed in respiration chambers for the measurement of indicator amino acid oxidation (LAAO) during a primed, constant infusion of L-[l-i C]pheEylalanine and, simultaneously, heat production (HP). The study period consisted of, at minimum, 0.5 h of equilibration before 1.5 h of background measurements and 4 h of collection period. The gas exchange was recorded for O2, CO2, and CH in 1 min intervals. Expired CO2 and blood plasma were collected in 30 min intervals for determination of C enrichment. 

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