najoNanosystems: Physics, Chemistry, MathematicsНаносистемы: физика, химия, математика2220-80542305-7971Университет ИТМО10.17586/2220-8054-2021-12-5-598-602najo-541Research ArticlePHYSICSФИЗИКАEnergy relaxation in molecular systems containing salt ionsЭнергетическая релаксация в молекулярных системах, содержащих ионы солейBaranovM. A.BaranovM. A.

29, Saint Petersburg, 195251

baranovma1993@gmail.comVelichkoE. N.VelichkoE. N.

29, Saint Petersburg, 195251

velichko-spbstu@yandex.ruNepomnyashchayaE. K.NepomnyashchayaE. K.

29, Saint Petersburg, 195251

elina.nep@gmail.comPleshakovI. V.PleshakovI. V.

26 Politechnicheskaya str., Saint Petersburg, 194021

ivanple@yandex.ruPeter the Great St. Petersburg Polytechnic UniversityRussian FederationIoffe InstituteRussian Federation202105082025125598602Copyright © Baranov M.A., Velichko E.N., Nepomnyashchaya E.K., Pleshakov I.V., 20252025Baranov M.A., Velichko E.N., Nepomnyashchaya E.K., Pleshakov I.V.Baranov M.A., Velichko E.N., Nepomnyashchaya E.K., Pleshakov I.V.Данная работа распространяется под лицензией Creative Commons Attribution 4.0.This work is licensed under a Creative Commons Attribution 4.0 License.https://nanojournal.ifmo.ru/jour/article/view/541

In this paper, we consider relaxation processes in molecular systems containing single biomolecule and salt ions. The energy fluctuations in such systems were evaluated using computer simulations. The comparative analysis of the free energy dynamics of alanine, tryptophan, and albumin biomolecules in constructed molecular systems (aqueous solutions with different degrees of ionization) resulted in high influence of ionizing impurities on the full energy of the system and on the energy relaxation time. The results obtained can be used for development of hybrid micro and nanoelectronic devices with built-in biomolecular objects, for example, biochemical sensors, devices with microflow of liquids, technology for the preparation of molecular films, etc.

В данной работе рассматриваются релаксационные процессы в молекулярных системах, содержащих одиночные биомолекулы и ионы солей. Флуктуации энергии в таких системах оценивались с помощью компьютерного моделирования. Сравнительный анализ динамики свободной энергии биомолекул аланина, триптофана и альбумина в построенных молекулярных системах (водных растворах с разной степенью ионизации) показал высокое влияние ионизирующих примесей на полную энергию системы и время энергетической релаксации. Полученные результаты могут быть использованы для разработки гибридных микро- и наноэлектронных устройств со встроенными биомолекулярными объектами, например, биохимических сенсоров, устройств с микропотоком жидкостей, технологий приготовления молекулярных пленок и т.д.

самоорганизациябелкимолекулярная динамикабиомолекулярная электроникаэнергетическая релаксацияself-organizationproteinsmolecular dynamicsbiomolecular electronicsenergy relaxationThis research was funded by RSF, grant number No 21-72-20029. The results were obtained using computational resources of Peter the Great Saint Petersburg Polytechnic University Supercomputing Center (www.spbstu.ru). The Authors express their deep gratitude to Prof. O. Yu. Tsybin for many fruitful discussions and invaluable advices which have helped us to plan the experiments and explain experimental data.ReferencesZotti L.A. Molecular Electronics. Applied Sciences, 2021, 11, P. 4828.Zotti L.A. Molecular Electronics. Applied Sciences, 2021, 11, P. 4828.Wang Y., Harrison C.B., Schulten K., McCammon J.A. Implementation of accelerated molecular dynamics in NAMD. Comput. Sci. Discov., 2011, P. 4.Wang Y., Harrison C.B., Schulten K., McCammon J.A. Implementation of accelerated molecular dynamics in NAMD. Comput. Sci. Discov., 2011, P. 4.Viloria J.S., Allega M.F., Lambrughi M., Papaleo E. An optimal distance cutoff for contact-based Protein Structure Networks using side-chain centers of mass. Sci. Rep., 2017, 7, P 1–11.Viloria J.S., Allega M.F., Lambrughi M., Papaleo E. An optimal distance cutoff for contact-based Protein Structure Networks using side-chain centers of mass. Sci. Rep., 2017, 7, P 1–11.Petty M.C., Nagase T., Suzuki H., Naito H. Molecular electronics. Springer Handbooks, 2017, 1.Petty M.C., Nagase T., Suzuki H., Naito H. Molecular electronics. Springer Handbooks, 2017, 1.Hasani H.J., Ganesan A., Ahmed M., Barakat K.H. Effects of protein-protein interactions and ligand binding on the ion permeation in KCNQ1 potassium channel. PLoS One, 2018, 13.Hasani H.J., Ganesan A., Ahmed M., Barakat K.H. Effects of protein-protein interactions and ligand binding on the ion permeation in KCNQ1 potassium channel. PLoS One, 2018, 13.Baranov M., Tsybin O. and Velichko E. Structured biomolecular films for microelectronics. Saint Petersbg. Polytech. State Univ.Journal. Phys. Math., 2021, 14, P. 85–99.Baranov M., Tsybin O. and Velichko E. Structured biomolecular films for microelectronics. Saint Petersbg. Polytech. State Univ.Journal. Phys. Math., 2021, 14, P. 85–99.Bibi F., Villain M., Guillaume C., Sorli B., Gontard N.A. Review: Origins of the Dielectric Properties of Proteins and Potential Development as Bio-Sensors. Sensors, 2016, 16(8), P. 1232.Bibi F., Villain M., Guillaume C., Sorli B., Gontard N.A. Review: Origins of the Dielectric Properties of Proteins and Potential Development as Bio-Sensors. Sensors, 2016, 16(8), P. 1232.Taylor P.A., Jayaraman A. Molecular Modeling and Simulations of Peptide-Polymer Conjugates Annu. Rev. Chem. Biomol. Eng., 2020, 11, P. 257–76.Taylor P.A., Jayaraman A. Molecular Modeling and Simulations of Peptide-Polymer Conjugates Annu. Rev. Chem. Biomol. Eng., 2020, 11, P. 257–76.Xiao B.L., Ning Y.N., Niu N.N., Li D., Moosavi-Movahedi A.A., Sheibani N., Hong J. Steered molecular dynamic simulations of conformational lock of Cu, Zn-superoxide dismutase. Sci. Rep., 2019, 9, P. 1-11.Xiao B.L., Ning Y.N., Niu N.N., Li D., Moosavi-Movahedi A.A., Sheibani N., Hong J. Steered molecular dynamic simulations of conformational lock of Cu, Zn-superoxide dismutase. Sci. Rep., 2019, 9, P. 1-11.Tavanti F., Pedone A., Menziani M.C. A closer look into the ubiquitin corona on gold nanoparticles by computational studies. New J. Chem., 2015, 39, P. 2474–82.Tavanti F., Pedone A., Menziani M.C. A closer look into the ubiquitin corona on gold nanoparticles by computational studies. New J. Chem., 2015, 39, P. 2474–82.Tavanti F., Pedone A. and Menziani M. C. Competitive Binding of Proteins to Gold Nanoparticles Disclosed by Molecular Dynamics Simulations J. Phys. Chem. C, 2015, 119, 22172-80Tavanti F., Pedone A. and Menziani M. C. Competitive Binding of Proteins to Gold Nanoparticles Disclosed by Molecular Dynamics Simulations J. Phys. Chem. C, 2015, 119, 22172-80Baranov M., Velichko E., Rozov S. Dehydrated films of protein solutions: structural properties. Saint Petersbg. Polytech. State Univ. Journal. Phys. Math- ematics, 2019, 12, P. 25–37.Baranov M., Velichko E., Rozov S. Dehydrated films of protein solutions: structural properties. Saint Petersbg. Polytech. State Univ. Journal. Phys. Math- ematics, 2019, 12, P. 25–37.Dyubo D., Tsybin O.Y., Baranov M.A., Alekseenko A.P., Velichko E.N. Study of electric properties of self-assembled films of albumin during their dehydration Recent citations Study of electric properties of self-assembled films of albumin during their dehydration. J. Phys, 2018, 1124, P. 31013.Dyubo D., Tsybin O.Y., Baranov M.A., Alekseenko A.P., Velichko E.N. Study of electric properties of self-assembled films of albumin during their dehydration Recent citations Study of electric properties of self-assembled films of albumin during their dehydration. J. Phys, 2018, 1124, P. 31013.Phillips J.C., Braun R., Wang W., Gumbart J., Tajkhorshid E., Villa E., Chipot C., Skeel R. D., Kal´e L., Schulten K. Scalable molecular dynamics with NAMD. J. Comput. Chem., 2005, 26, P. 1781–802.Phillips J.C., Braun R., Wang W., Gumbart J., Tajkhorshid E., Villa E., Chipot C., Skeel R. D., Kal´e L., Schulten K. Scalable molecular dynamics with NAMD. J. Comput. Chem., 2005, 26, P. 1781–802.Sanchez C., Galo G.J., Ribot F. and Grosso D. Design of functional nano-structured materials through the use of controlled hybrid organicinorganic interfaces. Comptes Rendus Chim., 2003, 6, P. 1131-51.Sanchez C., Galo G.J., Ribot F. and Grosso D. Design of functional nano-structured materials through the use of controlled hybrid organicinorganic interfaces. Comptes Rendus Chim., 2003, 6, P. 1131-51.

The authors declare that there are no conflicts of interest present.