Helix-capping interaction in λ cro protein: A free energy simulation analysis

1994 ◽  
Vol 19 (4) ◽  
pp. 310-323 ◽  
Author(s):  
Bruce Tidor
Keyword(s):  
Free Energy ◽  
Simulation Analysis ◽  
Protein A ◽  
Energy Simulation ◽  
Helix Capping ◽  
Cro Protein

Quantum Chemical and Free Energy Simulation Analysis of Retinal Conformational Energetics

1997 ◽  
Vol 37 (6) ◽  
pp. 1018-1024 ◽  
Author(s):  
Jérôme Baudry ◽  
Serge Crouzy ◽  
Benoît Roux ◽  
Jeremy C. Smith
Keyword(s):  
Free Energy ◽  
Quantum Chemical ◽  
Simulation Analysis ◽  
Energy Simulation

Solvent effect on the anomeric equilibrium in D-glucose: a free energy simulation analysis

1991 ◽  
Vol 113 (5) ◽  
pp. 1553-1557 ◽  
Author(s):  
Sookhee Ha ◽  
Jiali Gao ◽  
Bruce Tidor ◽  
John W. Brady ◽  
Martin Karplus
Keyword(s):  
Free Energy ◽  
Solvent Effect ◽  
Simulation Analysis ◽  
Energy Simulation

Determination of Base Flipping Free Energy Landscapes from Nonequilibrium Stratification

2019 ◽  
Author(s):  
Xiaohui Wang ◽  
Zhaoxi Sun
Keyword(s):  
Free Energy ◽  
Energy Landscape ◽  
Sampling Technique ◽  
Umbrella Sampling ◽  
Energy Simulation ◽  
Nonlinear Dependence ◽  
Free Energy Landscape ◽  
Convergence Criterion ◽  
Base Flipping ◽  
Convergence Behavior

<p>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 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 equilibrium umbrella sampling and nonequilibrium stratification is given. The results show that nonequilibrium free energy simulation is able to give 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 behavior 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. </p>

Energy Consumption Analysis on Office Building Ventilation

2012 ◽  
Vol 516-517 ◽  
pp. 1139-1143
Author(s):  
Ke Chun Sun ◽  
Wei Jun Zhang
Keyword(s):  
Energy Consumption ◽  
Energy Saving ◽  
Air Conditioning ◽  
Room Temperature ◽  
Simulation Analysis ◽  
Simulation Software ◽  
Energy Simulation ◽  
Office Building ◽  
Saving Effect ◽  
Night Ventilation

Chongqing weather conditions as the representative, energy simulation software DesT-c Chongqing office building energy simulation analysis, simulated natural building under different ventilation conditions at room temperature, the energy consumption of building cooling load and air-conditioning system changes, with an emphasis on energy-saving effect of the night ventilation; The study showed that in Chongqing reasonable use of ventilation reduce building natural room temperature to a certain extent; Sensitive indicators of building air conditioning energy consumption than the heating energy consumption of ventilation was significantly; Night ventilation when the number of ventilators is less than 5 times / h, the energy saving effect is very significant.

scholarly journals Determination of Base Flipping Free Energy Landscapes from Nonequilibrium Stratification

2018 ◽  
Author(s):  
Xiaohui Wang ◽  
Zhaoxi Sun
Keyword(s):  
Free Energy ◽  
Energy Landscape ◽  
Sampling Technique ◽  
Umbrella Sampling ◽  
Energy Simulation ◽  
Nonlinear Dependence ◽  
Free Energy Landscape ◽  
Convergence Criterion ◽  
Base Flipping ◽  
Convergence Behavior

<p>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 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 equilibrium umbrella sampling and nonequilibrium stratification is given. The results show that nonequilibrium free energy simulation is able to give 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 behavior 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. </p>

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