Free energy calculations may provide vital information for studying various chemical and biological processes.Quantum mechanical methods are required to accurately describe interaction energies,but their computations ...Free energy calculations may provide vital information for studying various chemical and biological processes.Quantum mechanical methods are required to accurately describe interaction energies,but their computations are often too demanding for conformational sampling.As a remedy,level correction schemes that allow calculating high level free energies based on conformations from lower level simulations have been developed.Here,we present a variation of a Monte Carlo(MC)resampling approach in relation to the weighted histogram analysis method(WHAM).We show that our scheme can generate free energy surfaces that can practically converge to the exact one with sufficient sampling,and that it treats cases with insufficient sampling in a more stable manner than the conventional WHAM-based level correction scheme.It can also provide a guide for checking the uncertainty of the levelcorrected surface and a well-defined criterion for deciding the extent of smoothing on the free energy surface for its visual improvement.We demonstrate these aspects by obtaining the free energy maps associated with the alanine dipeptide and proton transfer network of the KillerRed protein in explicit water,and exemplify that the MC resampled WHAM scheme can be a practical tool for producing free energy surfaces of realistic systems.展开更多
In the paper, an approach is proposed for the problem of consistency in depth maps estimation from binocular stereo video sequence. The consistent method includes temporal consistency and spatial consistency to elimin...In the paper, an approach is proposed for the problem of consistency in depth maps estimation from binocular stereo video sequence. The consistent method includes temporal consistency and spatial consistency to eliminate the flickering artifacts and smooth inaccuracy in depth recovery. So the improved global stereo matching based on graph cut and energy optimization is implemented. In temporal domain, the penalty function with coherence factor is introduced for temporal consistency, and the factor is determined by Lucas-Kanade optical flow weighted histogram similarity constraint(LKWHSC). In spatial domain, the joint bilateral truncated absolute difference(JBTAD) is proposed for segmentation smoothing. The method can smooth naturally and uniformly in low-gradient region and avoid over-smoothing as well as keep edge sharpness in high-gradient discontinuities to realize spatial consistency. The experimental results show that the algorithm can obtain better spatial and temporal consistent depth maps compared with the existing algorithms.展开更多
基金supported by the Mid-career Researcher Program(No.2017R1A2B3004946)through National Research Foundationfunded by Ministry of Science and ICT of Korea.
文摘Free energy calculations may provide vital information for studying various chemical and biological processes.Quantum mechanical methods are required to accurately describe interaction energies,but their computations are often too demanding for conformational sampling.As a remedy,level correction schemes that allow calculating high level free energies based on conformations from lower level simulations have been developed.Here,we present a variation of a Monte Carlo(MC)resampling approach in relation to the weighted histogram analysis method(WHAM).We show that our scheme can generate free energy surfaces that can practically converge to the exact one with sufficient sampling,and that it treats cases with insufficient sampling in a more stable manner than the conventional WHAM-based level correction scheme.It can also provide a guide for checking the uncertainty of the levelcorrected surface and a well-defined criterion for deciding the extent of smoothing on the free energy surface for its visual improvement.We demonstrate these aspects by obtaining the free energy maps associated with the alanine dipeptide and proton transfer network of the KillerRed protein in explicit water,and exemplify that the MC resampled WHAM scheme can be a practical tool for producing free energy surfaces of realistic systems.
基金the Science and Technology Innovation Project of Ministry of Culture of China(No.2014KJCXXM08)the National Key Technology Research and Development Program of the Ministry of Science and Technology of China(No.2012BAH37F02)the National High Technology Research and Development Program(863)of China(No.2011AA01A107)
文摘In the paper, an approach is proposed for the problem of consistency in depth maps estimation from binocular stereo video sequence. The consistent method includes temporal consistency and spatial consistency to eliminate the flickering artifacts and smooth inaccuracy in depth recovery. So the improved global stereo matching based on graph cut and energy optimization is implemented. In temporal domain, the penalty function with coherence factor is introduced for temporal consistency, and the factor is determined by Lucas-Kanade optical flow weighted histogram similarity constraint(LKWHSC). In spatial domain, the joint bilateral truncated absolute difference(JBTAD) is proposed for segmentation smoothing. The method can smooth naturally and uniformly in low-gradient region and avoid over-smoothing as well as keep edge sharpness in high-gradient discontinuities to realize spatial consistency. The experimental results show that the algorithm can obtain better spatial and temporal consistent depth maps compared with the existing algorithms.
