The microscopic mechanisms of ion hydration and ion selectivity in biomolecular systems are long-standing research topics, in which the difficulty is how to reasonably and accurately describe the ion-water and ion-bio...The microscopic mechanisms of ion hydration and ion selectivity in biomolecular systems are long-standing research topics, in which the difficulty is how to reasonably and accurately describe the ion-water and ion-biomolecule interactions. This paper summarizes the development and applications of the atom-bond electronegativity equalization fluctuating charge force field model, ABEEM/MM, in the investigations of ion hydration, metalloproteins and ion-DNA bases systems. Based on high-level quantum chemistry calculations, the parameters were optimized and the molecular potential functions were constructed and applied to studies of structures, activities, energetics, and thermodynamic and kinetic properties of these ion-containing sys- tems. The results show that the performance of ABEEM]MM is generally better than that of the common force fields, and its accuracy can reach or approach that of the hlgh-level ab initio MP2 method. These studies provide a solid basis for further investigations of ion selectivity in biomolecular systems, the structures and properties of metalloproteins and other related ion-containing systems.展开更多
This paper posits that we are living in a computer simulation to simulate physical reality which has the same computer simulation process as virtual reality (computer-simulated reality). The computer simulation proces...This paper posits that we are living in a computer simulation to simulate physical reality which has the same computer simulation process as virtual reality (computer-simulated reality). The computer simulation process involves the digital representation of data, the mathematical computation of the digitized data in geometric formation and transformation in space-time, and the selective retention of events in a narrative. Conventional physics cannot explain physical reality clearly, while computer-simulated physics can explain physical reality clearly by using the computer simulation process consisting of the digital representation component, the mathematical computation component, and the selective retention component. For the digital representation component, the three intrinsic data (properties) are rest mass-kinetic energy, electric charge, and spin which are represented by the digital space structure, the digital spin, and the digital electric charge, respectively. The digital representations of rest mass and kinetic energy are 1 as attachment space for the space of matter and 0 as detachment space for the zero-space of matter, respectively, to explain the Higgs field, the reverse Higgs field, quantum mechanics, special relativity, force fields, dark matter, and baryonic matter. The digital representations of the exclusive and the inclusive occupations of positions are 1/2 spin fermion and integer spin boson, respectively, to explain spatial translation by supersymmetry transformation and dark energy. The digital representations of the allowance and the disallowance of irreversible kinetic energy are integral electric charges and fractional electric charges, respectively, to explain the confinements of quarks and quasiparticles. For the mathematical computation component, the mathematical computation involves the reversible multiverse and oscillating M-theory as oscillating membrane-string-particle whose space-time dimension (D) number oscillates between 11D and 10D and between 10D and 4D to explain cosmology. For the selective retention component, gravity, the strong force, electromagnetism, and the weak force are the retained events during the reversible four-stage evolution of our universe, and are unified by the common narrative of the evolution.展开更多
基金supported by the National Natural Science Foundation of China(21133005 and 20703022)
文摘The microscopic mechanisms of ion hydration and ion selectivity in biomolecular systems are long-standing research topics, in which the difficulty is how to reasonably and accurately describe the ion-water and ion-biomolecule interactions. This paper summarizes the development and applications of the atom-bond electronegativity equalization fluctuating charge force field model, ABEEM/MM, in the investigations of ion hydration, metalloproteins and ion-DNA bases systems. Based on high-level quantum chemistry calculations, the parameters were optimized and the molecular potential functions were constructed and applied to studies of structures, activities, energetics, and thermodynamic and kinetic properties of these ion-containing sys- tems. The results show that the performance of ABEEM]MM is generally better than that of the common force fields, and its accuracy can reach or approach that of the hlgh-level ab initio MP2 method. These studies provide a solid basis for further investigations of ion selectivity in biomolecular systems, the structures and properties of metalloproteins and other related ion-containing systems.
文摘This paper posits that we are living in a computer simulation to simulate physical reality which has the same computer simulation process as virtual reality (computer-simulated reality). The computer simulation process involves the digital representation of data, the mathematical computation of the digitized data in geometric formation and transformation in space-time, and the selective retention of events in a narrative. Conventional physics cannot explain physical reality clearly, while computer-simulated physics can explain physical reality clearly by using the computer simulation process consisting of the digital representation component, the mathematical computation component, and the selective retention component. For the digital representation component, the three intrinsic data (properties) are rest mass-kinetic energy, electric charge, and spin which are represented by the digital space structure, the digital spin, and the digital electric charge, respectively. The digital representations of rest mass and kinetic energy are 1 as attachment space for the space of matter and 0 as detachment space for the zero-space of matter, respectively, to explain the Higgs field, the reverse Higgs field, quantum mechanics, special relativity, force fields, dark matter, and baryonic matter. The digital representations of the exclusive and the inclusive occupations of positions are 1/2 spin fermion and integer spin boson, respectively, to explain spatial translation by supersymmetry transformation and dark energy. The digital representations of the allowance and the disallowance of irreversible kinetic energy are integral electric charges and fractional electric charges, respectively, to explain the confinements of quarks and quasiparticles. For the mathematical computation component, the mathematical computation involves the reversible multiverse and oscillating M-theory as oscillating membrane-string-particle whose space-time dimension (D) number oscillates between 11D and 10D and between 10D and 4D to explain cosmology. For the selective retention component, gravity, the strong force, electromagnetism, and the weak force are the retained events during the reversible four-stage evolution of our universe, and are unified by the common narrative of the evolution.
