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用分子动力学模拟对改性寡核酸进行热力学参数估计

Soon Woo Park1, Junehawk Lee2, Jung Woo Park2

  • 1Center for Nanotubes and Nanostructured Composites, Sungkyunkwan University, Suwon 16419, Republic of Korea.

The journal of physical chemistry. B
|March 7, 2025
PubMed
概括

这项研究使用分子动力学模拟来准确预测RNA/DNA混合体的热力学参数. 分子力学通用化Born表面积 (MMGBSA) 方法显示改性核酸的性能优越,有助于治疗设计.

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Protons and neutrons, collectively called nucleons, are packed together tightly in a nucleus. With a radius of about 10−15 meters, a nucleus is quite small compared to the radius of the entire atom, which is about 10−10 meters. Nuclei are extremely dense compared to bulk matter, averaging 1.8 × 1014 grams per cubic centimeter. If the earth’s density were equal to the average nuclear density, the earth’s radius would be only about 200 meters.
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Nuclear Binding Energy

The difference between the calculated and experimentally measured masses is known as the mass defect of the atom. In the case of helium-4, the mass defect indicates a “loss” in mass of 4.0331 amu – 4.0026 amu = 0.0305 amu. The loss in mass accompanying the formation of an atom from protons, neutrons, and electrons is due to the conversion of that mass into energy that is evolved as the atom forms. The nuclear binding energy is the energy produced when the atoms’ nucleons are bound together;...
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Nuclear Fission

Many heavier elements with smaller binding energies per nucleon can decompose into more stable elements that have intermediate mass numbers and larger binding energies per nucleon—that is, mass numbers and binding energies per nucleon that are closer to the “peak” of the binding energy graph near 56. Sometimes neutrons are also produced. This decomposition of a large nucleus into smaller pieces is called fission. The breaking is rather random with the formation of a large number of different...
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Nuclear Transmutation

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Nuclear Overhauser Enhancement (NOE)

Irradiation of a spin-active nucleus causes an increase or decrease in the signal intensity of neighboring nuclei that are not necessarily chemically bonded or involved in J-coupling. This phenomenon, called the nuclear Overhauser enhancement (NOE), results from through-space interactions between the nuclear spins. The NOE effect decreases with increasing internuclear distance and is generally not observed beyond 4 angstroms. In NOE, dipole-dipole interactions between neighboring spin-active...