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Высокомолекулярные соединения (серия С), 2023, T. 65, № 1, стр. 91-109

ИСТОРИЯ И ПЕРСПЕКТИВЫ АТОМИСТИЧЕСКОГО МОДЕЛИРОВАНИЯ ПОЛИСАХАРИДОВ

В. И. Дещеня a, b, *, Н. Д. Кондратюк a, b, c

a Московский физико-технический институт (национальный исследовательский университет)
141701 Московская обл., Долгопрудный, Институтский пер., 9, Россия

b Объединенный институт высоких температур Российской академии наук
125412 Москва, ул. Ижорская, 13, стр.2, Россия

c Национальный исследовательский университет Высшая школа экономики
101000 Москва, ул. Мясницкая, 20, Россия

* E-mail: deshchenia.vi@phystech.edu

Поступила в редакцию 17.04.2023
После доработки 09.06.2023
Принята к публикации 13.07.2023

Аннотация

Представлены история и перспективы развития потенциалов межатомного взаимодействия для моделирования молекулярных систем и, в частности, полисахаридов. Рассмотрены популярные семейства потенциалов, такие как CHARMM, GROMOS, AMBER и OPLS. Обозначены проблемы применимости данных моделей для мономеров сахаров: плохая воспроизводимость экспериментальных свойств и гиперагрегация при малых концентрациях. Также рассмотрены векторы развития данной области: модификация невалентных взаимодействий в потенциале и использование поляризуемых потенциалов. Продемонстрированы примеры применения атомистического моделирования полисахаридов в актуальных фундаментальных и промышленных задачах на примере целлюлозы. Приведены важные вычислительные работы, внесшие существенный вклад в понимание структуры и процессов, происходящих в кристалле целлюлозы. Кроме того, дан обзор доступных на сегодня масштабов времен и характерных размеров систем для моделирования в пакетах GROMACS, LAMMPS, OpenMM и AMBER для модели раствора сахарозы.

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