title: ÐÐµÑÐ¾Ð´Ð¸ÐºÐ° Ð¾ÑÐµÐ½ÐºÐ¸ Ð´Ð¾ÑÑÐ¸Ð¶ÐµÐ½Ð¸Ñ ÑÐ¾ÑÑÐ¾ÑÐ½Ð¸Ñ ÑÐ°Ð²Ð½Ð¾Ð²ÐµÑÐ¸Ñ Ð¼Ð¾Ð»ÐµÐºÑÐ»ÑÑÐ½Ð¾Ð¹ ÑÐ¸ÑÑÐµÐ¼Ñ Ð¿Ð¾ Ð´Ð°Ð½Ð½ÑÐ¼ Ð¼Ð¾Ð»ÐµÐºÑÐ»ÑÑÐ½Ð¾Ð¹ Ð´Ð¸Ð½Ð°Ð¼Ð¸ÐºÐ¸
title: Ð²ÑÐ¿ÑÑÐºÐ½Ð°Ñ ÐºÐ²Ð°Ð»Ð¸ÑÐ¸ÐºÐ°ÑÐ¸Ð¾Ð½Ð½Ð°Ñ ÑÐ°Ð±Ð¾ÑÐ° Ð±Ð°ÐºÐ°Ð»Ð°Ð²ÑÐ°
titleType: Subtitle
title: Methodology for assessing the achievement of the equilibrium state of a molecular system according to molecular dynamics data
Creators: name: ÐÐ°ÑÐ¾Ð², ÐÐ»Ð°Ð´Ð¸Ð¼Ð¸Ñ
Publisher: name: Ð¡Ð°Ð½ÐºÑ-ÐÐµÑÐµÑÐ±ÑÑÐ³ÑÐºÐ¸Ð¹ Ð¿Ð¾Ð»Ð¸ÑÐµÑÐ½Ð¸ÑÐµÑÐºÐ¸Ð¹ ÑÐ½Ð¸Ð²ÐµÑÑÐ¸ÑÐµÑ ÐÐµÑÑÐ° ÐÐµÐ»Ð¸ÐºÐ¾Ð³Ð¾
Year: 2024
Subjects: ÑÐ°Ð²Ð½Ð¾Ð²ÐµÑÐ¸Ðµ
Ð¼Ð¾Ð»ÐµÐºÑÐ»ÑÑÐ½Ð°Ñ ÑÐ¸ÑÑÐµÐ¼Ð°
Ð¼Ð°ÑÑÐ¸ÑÐ° ÑÐ°ÑÑÑÐ¾ÑÐ½Ð¸Ð¹
ÑÐ°Ð·Ð¾Ð²Ð¾Ðµ Ð¿ÑÐ¾ÑÑÑÐ°Ð½ÑÑÐ²Ð¾
ÑÐµÐ¿Ð»Ð¾Ð²Ð°Ñ ÐºÐ°ÑÑÐ°
equilibrium
molecular system
distance matrix
phase space
heat map

description: Ð¢ÐµÐ¼Ð° Ð²ÑÐ¿ÑÑÐºÐ½Ð¾Ð¹ ÐºÐ²Ð°Ð»Ð¸ÑÐ¸ÐºÐ°ÑÐ¸Ð¾Ð½Ð½Ð¾Ð¹ ÑÐ°Ð±Ð¾ÑÑ: Â«ÐÐµÑÐ¾Ð´Ð¸ÐºÐ° Ð¾ÑÐµÐ½ÐºÐ¸ Ð´Ð¾ÑÑÐ¸Ð¶ÐµÐ½Ð¸Ñ ÑÐ¾ÑÑÐ¾ÑÐ½Ð¸Ñ ÑÐ°Ð²Ð½Ð¾Ð²ÐµÑÐ¸Ñ Ð¼Ð¾Ð»ÐµÐºÑÐ»ÑÑÐ½Ð¾Ð¹ ÑÐ¸ÑÑÐµÐ¼Ñ Ð¿Ð¾ Ð´Ð°Ð½Ð½ÑÐ¼ Ð¼Ð¾Ð»ÐµÐºÑÐ»ÑÑÐ½Ð¾Ð¹ Ð´Ð¸Ð½Ð°Ð¼Ð¸ÐºÐ¸Â». ÐÐ°Ð½Ð½Ð°Ñ ÑÐ°Ð±Ð¾ÑÐ° Ð¿Ð¾ÑÐ²ÑÑÐµÐ½Ð° ÑÐ°Ð·ÑÐ°Ð±Ð¾ÑÐºÐµ Ð¼ÐµÑÐ¾Ð´Ð¸ÐºÐ¸ Ð¾ÑÐµÐ½ÐºÐ¸ ÑÐ¾ÑÑÐ¾ÑÐ½Ð¸Ð¹ ÑÐ°Ð²Ð½Ð¾Ð²ÐµÑÐ¸Ñ Ð¼Ð¾Ð»ÐµÐºÑÐ»ÑÑÐ½Ð¾Ð¹ ÑÐ¸ÑÑÐµÐ¼Ñ. Ð¦ÐµÐ»ÑÑ Ð´Ð°Ð½Ð½Ð¾Ð¹ ÑÐ°Ð±Ð¾ÑÑ ÑÐ²Ð»ÑÐµÑÑÑ Ð¾Ð¿ÑÐµÐ´ÐµÐ»Ð¸ÑÑ ÐºÑÐ¸ÑÐµÑÐ¸Ð¹ ÑÐ°Ð²Ð½Ð¾Ð²ÐµÑÐ¸Ñ ÑÐ¸ÑÑÐµÐ¼Ñ Ð¸ Ð¿ÑÐ¾Ð²ÐµÑÐ¸ÑÑ Ð¿Ð¾Ð²ÐµÐ´ÐµÐ½Ð¸Ðµ Ð¼Ð¾Ð»ÐµÐºÑÐ»ÑÑÐ½ÑÑ ÑÐ¸ÑÑÐµÐ¼ Ð² ÑÑÐ°Ð±Ð¸Ð»ÑÐ½Ð¾Ð¼ Ð¸ Ð½ÐµÑÑÐ°Ð±Ð¸Ð»ÑÐ½Ð¾Ð¼ ÑÐ¾ÑÑÐ¾ÑÐ½Ð¸Ð¸ Ð´Ð²ÑÐ¼Ñ Ð¼ÐµÑÐ¾Ð´Ð°Ð¼Ð¸ Ð¾Ð±ÑÑÐµÑÐ° ÑÐ¸ÑÑÐµÐ¼: Ð°ÑÐ¾Ð¼Ð°Ð¼Ð¸ Ð¸ Ð°Ð¼Ð¸Ð½Ð¾ÐºÐ¸ÑÐ»Ð¾ÑÐ½ÑÐ¼Ð¸ Ð¾ÑÑÐ°ÑÐºÐ°Ð¼Ð¸. ÐÐ»Ñ Ð´Ð¾ÑÑÐ¸Ð¶ÐµÐ½Ð¸Ñ Ð¿Ð¾ÑÑÐ°Ð²Ð»ÐµÐ½Ð½Ð¾Ð¹ ÑÐµÐ»Ð¸ Ð¸ÑÐ¿Ð¾Ð»ÑÐ·Ð¾Ð²Ð°Ð»Ð¸ÑÑ Ð¼ÐµÑÐ¾Ð´Ñ Ð¼Ð¾Ð»ÐµÐºÑÐ»ÑÑÐ½Ð¾Ð¹ Ð´Ð¸Ð½Ð°Ð¼Ð¸ÐºÐ¸. Ð¡ Ð¿Ð¾Ð¼Ð¾ÑÑÑ ÑÑÐ¸Ñ Ð¼ÐµÑÐ¾Ð´Ð¾Ð² Ð±ÑÐ»Ð¸ Ð¿Ð¾Ð»ÑÑÐµÐ½Ñ Ð¼Ð°ÑÑÐ¸ÑÑ ÑÐ°ÑÑÑÐ¾ÑÐ½Ð¸Ð¹, Ð³Ð¸ÑÑÐ¾Ð³ÑÐ°Ð¼Ð¼Ñ Ð¸ ÑÐµÐ¿Ð»Ð¾Ð²ÑÐµ ÐºÐ°ÑÑÑ Ð±ÐµÐ»ÐºÐ° TRP CAGE Ð¸ ÑÑÐ°Ð³Ð¼ÐµÐ½ÑÐ° G-ÐºÐ²Ð°Ð´ÑÑÐ¿Ð»ÐµÐºÑÐ° ÐÐÐ. ÐÑÐ»Ð¾ Ð¿Ð¾Ð»ÑÑÐµÐ½Ð¾, ÑÑÐ¾ ÑÐ°ÑÑÐµÑ ÑÐ¸ÑÑÐµÐ¼ Ð¾ÑÑÐ°ÑÐºÐ°Ð¼Ð¸ Ð½Ðµ Ð¸Ð¼ÐµÐµÑ ÑÐ¸Ð»ÑÐ½Ð¾Ð³Ð¾ Ð¾ÑÐ»Ð¸ÑÐ¸Ñ Ð¾Ñ ÑÐµÑÑÐ½Ð¾Ð³Ð¾ ÑÐ°ÑÑÐµÑÐ° Ð°ÑÐ¾Ð¼Ð°Ð¼Ð¸. Ð Ð´Ð°Ð»ÑÐ½ÐµÐ¹ÑÐµÐ¼ ÑÑÐ¾ Ð¼Ð¾Ð¶Ð½Ð¾ Ð¸ÑÐ¿Ð¾Ð»ÑÐ·Ð¾Ð²Ð°ÑÑ Ð´Ð»Ñ Ð¿Ð¾Ð»Ð½Ð¾ÑÐµÐ½Ð½Ð¾Ð¹ Ð¾ÑÐµÐ½ÐºÐ¸ ÑÐ¾ÑÑÐ¾ÑÐ½Ð¸Ñ ÑÐ°Ð²Ð½Ð¾Ð²ÐµÑÐ¸Ñ, ÐºÐ¾ÑÐ¾ÑÐ¾Ðµ Ð±ÑÐ´ÐµÑ ÑÑÐ¸ÑÐ°ÑÑ ÑÐºÐ¾Ð»ÑÐºÐ¾ ÑÐ¸ÑÑÐµÐ¼Ð° Ð½Ð°ÑÐ¾Ð´Ð¸ÑÑÑ Ð² ÑÑÐ°Ð±Ð¸Ð»ÑÐ½Ð¾Ð¼ ÑÐ¾ÑÑÐ¾ÑÐ½Ð¸Ð¸ Ð¸ Ð½Ð°ÑÐ¾Ð´Ð¸ÑÑÑ Ð»Ð¸ Ð¾Ð½Ð° Ð² Ð½ÐµÐ¼ Ð²Ð¾Ð¾Ð±ÑÐµ.
description: The topic of the final qualifying work: "Methodology for assessing the achievement of the equilibrium state of a molecular system according to molecular dynamics data." This work is devoted to the development of a methodology for assessing the states of equilibrium of a molecular system. The purpose of this work is to determine the criterion of the equilibrium of the system and to test the behavior of molecular systems in a stable and unstable state by two methods of calculating systems: atoms and amino acid residues. To achieve this goal, the me thods of molecular dynamics were used. Using these methods, distance matrices, histograms, and heat maps of the TRP CAGE protein and a fragment of the G-DNA quadruplex were obtained. It was found that the calculation of systems by residues does not differ much from the honest calculation by atoms. In the future, this can be used for a full assessment of the state of equality, which will count how long the system is in a stable state and whether it is in it at all.