Развитие теории сольватации на основе мультимасштабных методов
Диссертация
Бурное развитие молекулярных биотехнологий и наноинженерии ставит новые научные задачи перед теоретической физической химией растворов. На сегодняшний день существует определенный разрыв между большим количеством накопленных за последние десятилетия экспериментальных данных по сольватации различных молекулярных объектов и их теоретической интерпретацией. До сих пор не создано общих теоретических… Читать ещё >
Список литературы
- Е. Westhof, editor Water and Biological Macromolecules. — The Macmillan press Ltd, 1993.
- Г. H. Чуев, M. В. Базилевский, Молекулярные модели сольватации в полярных жидкостях//Успехи химии- 2003.- Vol. 72, р. 827.
- P. R. Schleyer, editor Encyclopedia of Computational Chemistry. John Wiley & Sons, Chichester, UK, 1998.
- D. Reith, M. Putz, F. Muller-Plathe, Deriving effective mesoscale potentials from atomistic simulations// Journal of Computational Chemistry- October 2003.- Vol.24, № 13.- p. 1624−1636.
- I. Daubechies, Ten Lectures on Wavelets. V. 61 of CBMS/NSF Series in Applied Mathematics SIAM, Philadelphia, 1992.
- G. N. Chuev, M. V. Fedorov, N. Russo, Density functional study of polarons and bipolarons in polar liquids//Physical Review B- March 2003.- Vol.67, № 12 p. 125 103.
- G. N. Chuev, M. V. Fedorov, Density functional method based on wavelets for quantum-classical systems//Nternational Journal of Quantum Chemistry 2004. — Vol. 100, №.- p. 539−547.
- W. Kohn, L. J. Sham, Self-consistent equations including exchange and correlation effects//Physical Review A- 1965.- Vol. 140, p. 1133−1138.
- R. Evans, Nature of the liquid-vapor interface and other topics in the statistical-mechanics of nonuniform, classical fluids// Advances in Physics-1979.- Vol.28, №- p. 143−200.
- R. G. Parr, W. Yang, Density-Functional Theory of Atoms and Molecules. -Oxford University Press, New York, 1989.
- J.K. Percus, Recent Developments and Applications of Modern Density Functional Theory. Elsevier, Amsterdam, 1996.
- M. Schmidt, H. Lowen, J. M. Brader, R. Evans, Density functional for a model colloid-polymer mixture//Physical Review Letters- 2000.- Vol.85, p. 19 341 937.
- J. Jortner, R. M. Noyes, Some thermodynamic properties of the hydrated electron//Journal of Physical Chemistry- 1966. Vol. 70, p. 770−774.
- J. Jortner, N.R. Kestner, Electrons in Fluids. Springer, Berlin, 1973.
- Э. Д. Харт, M. Анбар, Гидратированный электрон. Атомиздат, Москва, 1973.
- L. Kevan, D. F. Feng, Theoretical models for solvated electrons// Chemical Reviews- 1980.- Vol.80, № 1- p. 1−20.
- А. К. Пикаев, Современная радиационная химия. Радиолиз газов и жидкостей. Наука, Москва, 1986.
- Н. P. Kaukonen, R. N. Barnett, U. Landman, Dielectrons in water clusters// Journal of Chemical Physics- 1992.- Vol. 97, № 2.- p. 1365−1377.
- V. D. Lakhno, G. N. Chuev, Structure of strong-coupled large polaron // Uspekhi Fizicheskikh Nauk- 1995.- Vol. 165, № 3- p. 285−298.
- M. Sprik, M. L. Klein, Optimization of a distributed gaussian-basis set using simulated annealing — application to the solvated electron // Journal of Chemical Physics- November 1987.- Vol.87, № 10 p.5987−5999.
- M. Sprik, R. W. Impey, M. L. Klein, Study of electron solvation in polar-solvents using path integral calculations// Journal of Statistical Physics- June 1986.- Vol.43, № 5−6.- p.967−972.
- G. J. Martyna, Z. Deng, M. L. Klein, Quantum simulation studies of singlet and triplet bipolarons in liquid ammonia// Journal of Chemical Physics 1993. — Vol.98, № 1- p.555−563.
- Г. H. Чуев, Статистическая физика сольватированного электрона//Успехи Физических Наук- 1999.- Vol. 169, р. 155−170.
- G. N. Chuev, V. V. Sychyov, Mean-field theory of an electron solvated in molten salts//Journal of Chemical Physics- March 2000.- Vol. 112, № 10-p.4707−4715.
- Г. Н. Чуев, Биполяроны в расплаве КС1 // Журнал экспериментальной и теоретической физики- 2000.- Vol. 118, р. 1134−1142.
- G. N. Chuev, V. V. Sychyov, О. Y. Sokolova, Mean-field treatment of polarons in strong electrolytes// Physical Review E- June 2001.- Vol.63, № 6 p. 61 204.
- D. Chandler, J. D. Mccoy, S. J. Singer, Density functional theory of nonuniform polyatomic systems. 2. Rational closures for integral-equations// Journal of Chemical Physics- November 1986.- Vol.85, № 10 p.5977−5982.
- D. Chandler, J. D. Mccoy, S. J. Singer, Density functional theory of nonuniform polyatomic systems. 1. General formulation// Journal of Chemical Physics -1986.- Vol.85, № 10 p.5971−5976.
- D. Laria, D. Wu, D. Chandler, Reference interaction site model polaron theory of the hydrated electron// Journal of Chemical Physics- September 1991. — Vol. 95, № 6.- p. 4444−4453.
- J.-P. Hansen, I. R. McDonald, Theory of Simple Liquids, 4th ed., 2000.
- T. Sumi, T. Imai, F. Hirata, Integral equations for molecular fluids based on the interaction site model: Density-functional formulation // Journal of Chemical Physics- 2001.- Vol.115, № 14.- p. 6653−6662.
- R. Ramirez, R. Gebauer, M. Mareschal, D. Borgis, Density functional theory of solvation in a polar solvent: Extracting the functional from homogeneous solvent simulations//Physical Review E- September 2002.- Vol.66, № 3 p. 31 206.
- R. Ramirez, M. Mareschal, D. Borgis, Direct correlation functions and the density functional theory of polar solvents // Chemical Physics December 2005.- Vol.319, № 1−3.- p.261−272.
- G. A. Jeffrey, W. Saenger, Hydrogen Bonding in Biological Structures. -Springer-Verlag, Berlin, 1991.
- S. G. Zhang, M. Altman, Peptide self-assembly in functional polymer science and engineering//Reactive and Functional Polymers- July 1999.- Vol.41, № 1−3 p. 91−102.
- S. G. Zhang, Emerging biological materials through molecular self-assembly// Biotechnology Advances- December 2002.- Vol.20, № 5−6 p.321−339.
- S. G. Zhang, D. M. Marini, W. Hwang, S. Santoso, Design of nanostructured biological materials through self-assembly of peptides and proteins // Current Opinion in Chemical Biology- December 2002.- Vol.6, № 6 p.865−871.
- A. Aggeli, М. Bell, N. Boden, J. N. Keen, Т. С. В. McLeish, I. Nyrkova, S. E. Radford, A. Semenov, Engineering of peptide /5-sheet nanotapes// Journal of Materials Chemistry- July 1997.- Vol. 7, № 7.- p. 1135−1145.
- К. Биндер, editor Методы Монте-Карло в статистической физике-. Мир, Москва 1982.
- М. P. Allen, D. J. Tildesley, editors Computer Simulation of Liquids. -Clarendon Press, Oxford, 1987.
- X. Гулд, Я. Тобочник, Компьютерное моделирование в физике. В 2-х частях, ч.2. Мир, Москва, 1990.
- Г. Р. Иваницкий, С. И. Воробьев, Образование подвижных структур в кровотоке — основа функционирования перфторуглеродной «искусственной крови"//Биофизика- 1996.- Vol.41, р. 178−190.
- Г. Р. Иваницкий, С. И. Воробьев, Кровезаменитель «Перфторан"//Вестник РАН- 1997.- Vol.67, р.998−1008.
- И. Добеши, Десять лекций no вейвлетам. НИЦ «Регулярная и хаотическая динамика», Ижевск, 2001.
- В.П. Дьяконов, Вейвлеты. От теории к практике. Изд. Салон-Р, Москва, 2002.
- S. G. Mallat, A Wavelet Tour of Signal Processing. Academic press, San Diego, 1999.
- S. Goedecker, Wavelets and Their Application for the Solution of Partial Differential Equations in Physics. Presses Polytechniques et Universitaires Romandes, Lausanne, 1998.
- Y. Meyer, Wavelets: Algorithms and Applications. SIAM, Philadelphia, 1993.
- D. L. Donoho, De-noising by soft-thresholding // IEEE Transactions On Information Theory- MAY 1995.- Vol.41, № 3.- p.613−627.
- G. N. Chuev, N. Russo, Density functional theory of bipolarons in polar liquids //Chemical Physics Letters- January 2003.- Vol. 368, № 1−2.- p. 53−58.
- M. V. Fedorov, G. N. Chuev, Yu. A. Kuznetsov, E. G. Timoshenko, Wavelet treatment of the intrachain correlation functions of homopolymers in dilute solutions//Physical Review E- 2004.- Vol.70, № 5- p.51 803.
- A.B. Romeo, C. Horellou, J. Bergh, N-body simulations with two-orders-of-magnitude higher performance using wavelets//Monthly Notices of the Royal Astronomical Society- JUN 2003.- Vol.342, № 2 p.337−344.
- W. Sweldens, The lifting scheme: A custom-design construction of biorthogonal wavelets // Applied and Computational Harmonic Analysis-1996.- Vol.3, № 2.- p. 186−200.
- R. T. Ogden, Essential wavelets for statistical applications and data analysis. Birkhauser, Boston, 1997.
- D. L. Donoho, Unconditional bases are optimal bases for data compression and statistical estimation// Applied and Computational Harmonic Analysis-1993.- Vol.1, p. 100−115.
- D. L. Donoho, M. Vetterli, R. A. DeVore, I. Daubechies, Data compression and harmonic analysis//IEEE Transactions On Information Theory- 1998. — Vol. 44, № 6.- p. 2435−2476.
- H. J. Flad, W. Hackbusch, D. Kolb, R. Schneider, Wavelet approximation of correlated wave functions. I. Basics// Journal of Chemical Physics- 2002.-Vol. 116, № 22 p. 9641−9657.
- J. P. Antoine, P. Vandergheynst, Wavelets on the n-sphere and related manifold//Journal of Mathematical Physics- 1998.- Vol.39, № 8 p.3987−4008.
- K. Cho, T. A. Arias, J. D. Joannopoulos, P. K. Lam, Wavelets in electronic-structure calculations//Physical Review Letters- 1993.- Vol.71, № 12 p. 1808−1811.
- S. Goedecker, 0. Ivanov, Algorithms and applications — solution of multiscale partial differential equations using wavelets//Computers in Physics- 1998. — Vol. 12, № 6.- p. 548−555.
- S. W. Han, K. J. Cho, Ihm J., Wavelets in all-electron density-functional calculations//Physical Review В 1999.- Vol.60, M- p. 1437−1440.
- S. Goedecker, O. Ivanov, Frequency localization properties of the density matrix and its resulting hypersparsity in a wavelet representation // Physical Review B- 1999.- Vol.59, № 11.- p. 7270−7273.
- D. Barache, J. P. Antoine, J. M. Dereppe, The continuous wavelet transform, an analysis tool for NMR spectroscopy // Journal of Magnetic Resonance -1997.- Vol.128, № 1- p. 1−11.
- T. A. Arias, Multiresolution analysis of electronic structure: Semicardinal and wavelet bases//Reviews of Modern Physics- 1999.- Vol.71, № 1- p.267−311.
- H. J. Luo, D. Kolb, Flad H. J., W. Hackbusch, T. Koprucki, Wavelet approximation of correlated wave functions. II. Hyperbolic wavelets and adaptive approximation schemes// Journal of Chemical Physics- 2002, — Vol. 117, № 8 p. 3625−3638.
- В. Спиридонов, Самоподобие, всплески и квазикристаллы//Компьютерра 1998.- Vol.236, р.38−45.
- Р.С. Ivanov, M.G. Rosenblum, С.К. Peng, J. Mietus, S. Havlin, H.E. Stanley, A.L. Goldberger, Scaling behaviour of heartbeat intervals obtained by wavelet-based time-seriese analysis//Nature- 1996.- Vol.383, p. 323−327.
- P.C. Ivanov, L.A. Amaral, A.L. Goldenberger, Multifractality in human heartbeat dynamics//Nature- 1999.- Vol. 399, p. 461−465.
- И.Р. Стаховский, Вейвлетный анализ временных сейсмических рядов // ДАН- 1996.- Vol.350, р.393−396.
- К. С. Бураков, Д. К. Галягин, И. Е. Начасова, М. Ю. Решетняк, Д. Д. Соколов, П. Г. Фрик, Вейвлет-анализ вариаций напряженности геомагнитного поля за последние четыре тысячи лет//Изв. РАН, сер. Физика Земли 1998.- Vol. 34, р. 83−88.
- Д.К. Галягин, Д. М. Печерский, М. Ю. Решетняк, Д. Д. Соколов, П. Г. Фрик, Вейвлет-анализ характеристик геомагнитного поля в неогее//Изв. РАН, сер. Физика Земли- 2000.- Vol.36, р. 82−89.
- М. Шредер, Фракталы, хаос, временные законы. Пер. с англ. Ижевск: НИЦ «Регулярная и хаотическая динамика», 2001.
- A. Grossman, J. Morlet, Decomposition of hardy functions into square integrable wavelets of constant shape. // SIAM Journal on Mathematical Analysis- 1984.- Vol. 15, p. 2473−2479.
- Y. Meyer, Wavelets and applications. Proceedings of the International Conference on Wavelets, May 1989, Marseille, France- Masson, Paris, 1989.
- S. G. Mallat, A theory for multiresolution signal decomposition//IEEE Trans. On Pattern Analysis and Machine Intelligence PAMI-II- 1989.- Vol. 11, p. 674−693.
- К. Чуй, Введение в вэйвлеты. Мир, Москва, 2001.
- JI. Левкович-Маслюк, Дайджест вэйвлет-анализа, в двух формулах и 22 рисунках.//Компьютерра- 1998.- Vol. 236, р.31−37.
- В. И. Воробьев, В. Г. Грибунин, Теория и практика вейвлет-преобразования. ВУС, Санкт-Петербург, 1999.
- К. Tribouley, Practical density estimation using wavelet methods. Statistica Neerlandica, 1995.
- S.-Y. Huang, Density estimation by wavelet-based reproducing kernels // Statistica Sinica- 1999, — Vol.9, p. 137−151.
- O. Renaud, Density estimation with wavelets: Variability, invariance, and discriminant power // Technical Report, Statistics Department, Stanford University- 2000.-, p.2000−34.
- О. Renaud, The discrimination power of projection pursuit with different density estimators//Biometrika- 2002.- Vol.89, p. 129−143.
- B. Vidacovic, Statistical Modeling by Wavelets. New York, Wiley, 1999.
- D.B. Percival, A.T. Walden, Wavelet methods for time series analysis. -Cambridge University Press, Cambridge, UK, 2000.
- A. Arneodo, Б. Bacry, P.V. Graves, J. F. Muzy, Characterizing long-range correlations in DNA sequences from wavelet analysis//Physical Review Letters- 1995.- Vol.74, p. 3293−3296.
- A. Arneodo, B. Audit, E. Bacry, S. Manneville, J.F. Muzy, S.G. Roux, Thermodynamics of fractal signals based on wavelet analysis: Application to fully developed turbulence data and DNA sequences//Physica A- 1998. — Vol. 254, p. 24−45.
- S. Blanco, C.E. D’Attellis, S.I. Isaacson, O.A. Rosso, R.O. Sirne, Time-frequency analysis of electroencephalogram series. II. Gabor and wavelet transforms//Physical Review E- 1996.- Vol.54, p.6661−6672.
- S. Blanco, S. Kochen, O.A. Rosso, P. Saldalo, Applying tome — frequency analysis to seizure EEG activity//IEEE Engineering in Medicine and Biology- 1997.- Vol.16, p. 64−71.
- S. Thurner, M.C. Feurstein, M.C. Teich, Multiresolution wavelet analysis of heartbeat intervals discriminates healthy patients from those with cardiac pathology//Physical Review Letters- 1998.- Vol.80, p. 1554−1547.
- Y. Ishikawa, Wavelet Analysis for Clinical Medicine. Medical Publication, 2001.
- Ф.Ф. Дедус, C.A. Махортых, M.H. Устинин, А. Ф. Дедус, Обобщенный спектрально-аналитический метод обработки информационных массивов. Задачи анализа изображений и распознавания образов. Машиностроение, Москва, 1999.
- I. Daubechies, Orthogonal basis of compactly supported wavelets // Communication in Pure and Applied Mathematics- 1989.- Vol.41, p.909−996.
- J.-P. Hansen, I. R. McDonald, Theory of Simple Liquids, 2nd ed. Elsevier Science and Technology Books, first edition Jan 1990.
- A. Botti, F. Bruni, A. Isopo, M. A. Ricci, Soper A. K., Experimental determination of the site-site radial distribution functions of supercooled ultrapure bulk water//Journal of Chemical Physics- 2002.- Vol. 117, № 13-p.6196−6199.
- E Matteoli, G. A. Mansoori, A simple expression for radial-distribution functions of pure fluids and mixtures// Journal of Chemical Physics- 1995. — Vol. 103, № 11.- p. 4672−4677.
- S. Goldman, Explicit equation for the radial-distribution function of a dense leimard-jones fluid// Journal of Physical Chemistry- 1979.- Vol.83, № 23-p. 3033−3037.
- G. N. Chuev, M.V. Fedorov, Wavelet treatment of radial distribution functions of solutes//Physical Review E- AUG 2003.- Vol.68, № 2 p. 27 702.
- G. N. Chuev, M. V. Fedorov, Wavelet treatment of structure and thermodynamics of simple liquids // Journal of Chemical Physics January 2004.- Vol. 120, № 3- p. 1191−1196.
- G. N. Chuev, M. V. Fedorov, Wavelet algorithm for solving integral equations of molecular liquids, a test for the reference interaction site model// Journal of Computational Chemistry- August 2004.- Vol.25, № 11- p. 1369−1377.
- D. Chandler, H. C. Andersen, Optimized cluster expansions for classical fluids. 2. Theory of molecular liquids // Journal of Chemical Physics 1972. — Vol. 57, № 5 — p. 1930−1937.
- H. J. C. Berendsen, J. R. Grigera, T. P. Straatsma, The missing term in effective pair potentials// Journal of Physical Chemistry- November 1987.-Vol. 91, № 24, — p. 6269−6271.
- T. P. Straatsma, H. J. C. Berendsen, J. P. M. Postma, Free-energy of hydrophobic hydration — a molecular-dynamics study of noble-gases in water //Journal of Chemical Physics- 1986.- Vol.85, № 11.- p. 6720−6727.
- B. M. Pettitt, Rossky P. J., Alkali-halides in water-ion solvent correlations and ion-ion potentials of mean force at infinite dilution// Journal of Chemical Physics- MAY 1986.- Vol.84, № 10.- p.5836−5834.
- P. A. Monson, G. P. Morriss, Recent progress in the statistical-mechanics of interaction site fluids// Advances in Chemical Physics- 1990.- Vol. 77, p. 451−550.
- Jr. Marpl, Digital spectral analysis with applications. Prentice-Hall, New Jersey, 1987.
- M. В. Федоров, Сравнение формы «несостоятельных гистограмм» с помощью вейвлет-анализа//Биофизика- 2001.- Vol.46, р.790−794.
- М. В. Федоров, Метод идентификации форм распределений малых выборок// Российский химический журнал- 2002.- Vol. XLVI, р. 9−11.
- A. Santos, S. В. Yuste, М. L. Наго, Radial distribution functions for a multicomponent system of sticky hard spheres// Journal of Chemical Physics- 1998.- Vol.109, № 16.- p. 6814−6819.
- C.JI. Марпл-мл., Цифровой спектральный анализ и его приложения. -Мир, Москва, 1990.
- Е. G. Timoshenko, Y. A. Kuznetsov, R. Connolly, Intrachain correlation functions and shapes of homopolymers with different architectures in dilute solution//Journal of Chemical Physics- 2002.- Vol. 116, № 9.- p. 3905−3916.
- J Cloizeaux, G. Jannink, Polymers in Solution. Oxford Science, 1990.
- L. Schafer, U Lehr, С. Kappeler, Higher-order calculations of the renormalization-group flow for multicomponent polymer-solutions // Journal De Physique I- 1991.- Vol. 1, № 2, — p. 211−233.
- L. Schafer, Excluded volume effects in polymer solutions as explained by the Renormalisation Group. V. Chapter 16 Springer-Verlag, 1999.
- R. Guida, J. Zinn-Justin, Critical exponents of the N-vector model//Journal of Physics A-mathematical and General- 1998.- Vol.31, № 40.- p. 8103−8121.
- Y. A. Kuznetsov, Е. G. Timoshenko, On the conformational structure of a stiff homopolymer// Journal of Chemical Physics- 1999.- Vol. Ill, № 8 p. 3744−3752.
- E. G. Ganazzoli, Y. A. Kuznetsov, Conformations of amphiphilic diblock star copolymers//Macromolecular Theory and Simulations- 2001.- Vol. 10, № 4-p.325−338.
- S. Caracciolo, M. S. Causo, A. Pelissetto, End-to-end distribution function for dilute polymers//The Journal of Chemical Physics- 2000.- Vol. 112, № 17-p. 7693−7710.
- W. H. Press, S. A. Teukolsky, W. T. Vetterling, B. P. Flannery, Numerical Recipes in C. Cambridge University Press, 1992.130. http://www.gnuplot.info/.
- C. Ferber, A. Jusufi, M. Watzlawek, C. N. Likos, H. Lowen, Polydisperse star polymer solutions//Physical Review E- 2000.- Vol.62, № 5- p.6949−6956.
- C. Ferber, Y. Holovatch, Copolymer networks and stars: Scaling exponents// Physical Review E- 1997.- Vol.56, № 6.- p.6370−6386.
- A. Yethiraj, Density functional theory of polymers: A Curtin-Ashcroft type weighted density approximation//Journal of Chemical Physics- 1998.- Vol. 109, № 8 p. 3269−3275.
- C. N Patra, A. Yethiraj, Density functional theory for nonuniform polymers: Accurate treatment of the effect of attractive interactions// Journal of Chemical Physics- 2003.- Vol. 118, № 10.- p. 4702−4706.
- M. B. Sweatman, Weighted density approximation for bonding in molecules: Ring and cage polymers// Journal of Physics: Condensed Matter 2003. — Vol. 15, № 23 — p. 3875−3890.
- J. P. Hansen, G. Zerah, How reliable are integral-equations for the pair structure of binary fluid mixture//Physics Letters A- 1985. Vol. 108, № 5−6-p. 277−280.
- Г. H. Саркисов, Структурные модели воды // Успехи Физических Наук -2006, — Vol. 176, р. 833−845.
- B. Daguanno, R. Klein, Structural effects of polydispersity in charged colloidal dispersions// Journal of the Chemical Society — Faraday Transactions- 1991. Vol. 87, № 3 — p. 379−390.
- T. Ichiye, A. D. J. Haymet, Structural effects of polydispersity in charged colloidal dispersions// Journal of Chemical Physics- 1990.- Vol.93, № 12-p.8954−8962.
- R. K. Pandey, D. N. Tripathi, Analytical solution of the Ornstein-Zernike equation for the structure factor of ordered plasmas using sogami-ise potential //Journal of the Physical Society of Japan- 2004.- Vol.73, № 7- p. 17 481 753.
- H. Xu, J. P. Hansen, Density-functional theory of pair correlations in metallic hydrog//Physical Review E- 1998.- Vol.57, № 1.- p. 211−223.
- C. F. Strnadl, G. Kahl, The electronic density of states in liquids: Computer simulation versus integral-equation approach// Journal of Physics: Condensed Matter- 1993.- Vol.5, № 37, — p.6801−6818.
- M. Bebendorf, S. Rjasanov, Adaptive Low-Rank Approximation of Collocation Matrices//Computing- 2003.- Vol.70, № 1.- p. 1−24.
- E. E. Tyrtyshnikov, Incomplete cross approximation in the mosaic-skeleton method//Computing- 2000, — Vol.64, p.367−380.
- W. Hackbusch, B. N. Khoromskij, Low-rank kronecker product approximation to multi-dimensional nonlocal operators. I. Separable approximation of multivariate functions//Computing- 2006.- Vol.76, p. 177−202.
- W. Hackbusch, B. N. Khoromskij, Low-rank kronecker product approximation to multi-dimensional nonlocal operators. II. hkt representations of certain operators//Computing- 2006.- Vol.76, p.203−225.
- M. V. Fedorov, H. J. Flad, G. N. Chuev, L. Grasedyck, B. N. Khoromskij, A structured low-rank wavelet solver for the Ornstein-Zernike integral equation //Computing- May 2007.- Vol.80, № 1.- p.47−73.
- S. Labik, A. Malijevsky, P. Vonka, A rapidly convergent method of solving the Ornstein-Zernike equation//Molecular Physics- 1985.- Vol.56, № 3 p. 709−715.
- S. Labik, R. Pospiil, A. Malijevsky, W. R. Smith, An efficient gauss-newton-like method for the numerical solution of the Ornstein-Zernike integral equation for a class of fluid models// Journal of Computational Physics- 1994.- Vol. 115, № 1 p. 12−21.
- M. J. Gillan, New method of solving the liquid structure integral-equations// Molecular Physics- 1979.- Vol.38, № 6.- p. 1781−1794.
- W. Hackbusch, Multi-grid methods and Applications. Springer-Verlag, Berlin, 1985.
- C. T. Kelley, Iterative methods for linear and nonlinear equations. V. 16 of Frontiers in Applied Mathematics SIAM, Philadelphia, 1995.
- C. T. Kelley, B. M. Pettitt, A fast solver for the Ornstein-Zernike equations// Journal of Computational Physics- JUL 2004.- Vol. 197, № 2 p. 491−501.
- R.A. DeVore, S.V. Konyagin, V.N. Temlyakov, Hyperbolic wavelet approximation//Constructive Approximation 1998.- Vol. 14, № 1- p. 1−26.
- G. Deslauriers, S. Dubuc, Symmetric iterative interpolation processes // Constructive Approximation- 1989.- Vol.5, № 1- p.49−68.
- G. Beylkin, R. Coifman, V. Rokhlin, Fast wavelet transforms and numerical algorithms//Communications on Pure and Applied Mathematics MAR 1991. — Vol. 44, № 2.- p. 141−183.
- G. H. Golub, C. F. Loan, Matrix Computations. Johns Hopkins University Press, 1996.159. http://mathworks.com/.
- M. Kinoshita, M. Harada, Numerical-solution of the HNC equation for fluids of nonspherical particles: An efficient method with application to dipolar hard-spheres//Molecular Physics 1991.- Vol.74, p.443−464.
- G. Malescio, P. V. Giaquinta, Y. Rosenfeld, Iterative solutions of integral equations and structural stability of fluids.// Physical Review E- 1998. Vol. 57, p. R3723-R3726.
- R. Fantoni, G. Pastore, Stability of the iterative solutions of integral equations as one phase freezing criterion.//Physical Review E- 2003.- Vol.68, p. 4 046 104.
- A. T. Peplow, R. E. Beardmore, F. Bresme, Algorithms for the computation of solutions of the Ornstein-Zernike equation // Physical Review E 2006. -Vol. 74, p. 46 705.
- E. Sarkisov, The gas-liquid phase-transition singularities in the framework of the liquid-state integral equation formalism // Journal of Chemical Physics -2005.- Vol. 122, p. 214 504.
- L. Belloni, Inability of the hypernetted chain integral equation to exhibit a spinodal line//Journal of Chemical Physics- 1993.- Vol.98, p. 8080−8095.
- P. G. Ferreira, R. L. Carvalho, M. M. T. Dagama, A. G. Schlijper, Schlijper: Singularities in the consistent hypernetted-chain approximation.// Journal of Chemical Physics- 1994.- Vol. 101, p. 594−602.
- C. Caccamo, Integral equation theory description of phase equilibria in classical fluids//Physics Reports-Review Section of Physics Letters- 1996. Vol. 274, p. 1−105.
- W. Hackbusch, A sparse matrix arithmetic based on 7^-matrices. part i: Introduction to ^-matrices.//Computing- 1999.- Vol.62, p.89−108.
- W. Hackbusch, B. N. Khoromskij, A sparse «H-matrix arithmetic. II. Application to multi-dimensional problems//Computing- 2000, — Vol. 64, p. 21−47.
- L. Grasedyck, W. Hackbusch, Construction and arithmetics of H-matrices// Computing- 2003.- Vol.70, p.295−334.
- R. M. Dreizler, E. K. U. Gross, Density-Functional Theory: An Approach to the Quantum Many-Body Problem. Springer, Berlin, 1990.
- J. VandeVondele, M. Sprik, A molecular dynamics study of the hydroxyl radical in solution applying self-interaction-corrected density functional methods//Physical Chemistry Chemical Physics- 2005.- Vol.7, № 7 p. 1363−1367.
- J. C. Grossman, E. Schwegler, E. W. Draeger, F. Gygi, G. Galli, Towards an assessment of the accuracy of density functional theory for first principles simulations of water// Journal of Chemical Physics January 2004. — Vol. 120, № 1.- p. 300−311.
- R. Wieczorek, J. J. Dannenberg, Enthalpies of hydrogen-bonds in alpha-helical peptides, an ONIOM DFT/AM1 study// Journal of the American Chemical Society- October 2005.- Vol. 127, № 42.- p. 14 534−14 535.
- D. Y. C. Chan, Density functional theory of charged colloidal systems // Physical Review E- 2001.- Vol.63, p.61 806.
- G. Reddy, C. P. Lawrence, J. L. Skinner, A. Yethiraj, Liquid state theories for the structure of water// Journal of Chemical Physics- 2003.- Vol. 119, № 24-p. 13 012−13 016.
- S. J. Singer, D. Chandler, Free-energy functions in the extended rism approximation//Molecular Physics- 1985.- Vol. 55, № 3 p. 621−625.
- C. N. Chuev, M. V. Fedorov, H. J. Luo, D. Kolb, E. G. Timoshenko, 3d wavelet treatment of solvated bipolaron and polaron// Journal of Theoretical and Computational Chemistry- September 2005.- Vol.4, № 3 p. 751−767.
- S. Q. Wei, M. Y. Chou, Wavelets in self-consistent electronic structure calculations//Physical Review Letters- 1996.- Vol. 76, № 15 p. 2650−2653.
- T. Yanai, G. I. Fann, Z. Gan, R. J. Harrison, G. Beylkin, Multiresolution quantum chemistry in multiwavelet bases: Hartree-Fock exchange// Journal of Chemical Physics- 2004, — Vol. 121, № 14, — p. 6680−6688.
- A. D. Becke, Density-functional thermochemistry. III. The role of exact exchange//Journal of Chemical Physics- 1993.- Vol. 98, № 7.- p. 5648−5652.
- R. J. Bartlett, J. F. Stanton, Applications of post-hartree-fock methods: A tutorial//Reviews in Computational Chemistry- 1994.- Vol.5, p.65−169.
- R. J. Harrison, G. I. Fann, T. Yanai, Z. Gan, G. Beylkin, Multiresolution quantum chemistry: Basic theory and initial applications// Journal of Chemical Physics- December 2004.- Vol. 121, № 23 p. 11 587−11 598.
- S. Nagy, J. Pipek, Multiresolution analysis of density operators, electron density, and energy functionals//International Journal of Quantum Chemistry- September 2001.- Vol.84, № 5.- p.523−529.
- R. Schneider, T. Weber, Wavelets for density matrix computation in electronic structure calculation// Applied Numerical Mathematics October 2006. — Vol. 56, № 10−11.- p. 1383−1396.
- W. H. Press, S. A. Teukolsky, W. T. Vetterling, B. P. Flannery, Numerical Recipes in C. The Art of Scientific Computing. Cambridge University Press: New York, 1996.
- J.C. Thompson, Electrons in Liquid Ammonia. Oxford University Press, London, 1976.
- R. R. Dogonadze, E. Kalman, A. A. Kornyshev, J. Ulstrup, editors The Chemical Physics of Solvation. Part C. Elsevier, Amsterdam, 1988.
- J. Acrivos, Physics and Chemistry of Electrons and Ions in Condensed Matter.- Reidel, New York, 1984.
- G. N. Chuev, Statistical physics of the solvated electron//Uspekhi Fizicheskikh Nauk- 1999.- Vol. 169, № 2, — p. 155−170.
- J.H. Baxendale, F. Busi, The Study of Fast Processes and Transient Species by Electron Pulse Radiolysis. Reidel, Dordrecht, 1982.
- C. Ferradini, J. P. Jay-Gerin, Excess Electrons in Dielectric Media. Boca Raton: CRC Press, 1991.
- D. Chandler, K. Leung, Excess electrons in liquids geometrical perspectives //Annual Review of Physical Chemistry- 1994.- Vol.45, p. 557−591.
- J.-P. Hansen, I. R. McDonald, Theory of Simple Liquids, 1st ed. Academic, London, 1986.
- K. Iguchi, Theory of the solvated electron in polar liquids. I. Oriented dipole model//The Journal of Chemical Physics- 1968.- Vol.48, p. 1735−1738.
- W. M. Bartczak, M. Hilczer, J. Kroh, A statistical-model of the hydrated electron//Journal of Physical Chemistry- July 1987.- Vol.91, № 14 p. 3834−3840.
- J.W. Negele, H. Orland, Quantum Many-Particle Systems. Addison-Wesley, Redwood City, 1988.
- J. J. Zhu, R. I. Cukier, A mean-field theory of a localized excess electron in a polar fluid//Journal of Chemical Physics- October 1993.- Vol.99, № 7.- p. 5384−5395.
- W.C. Gottschall, E.J. Hart, The effect of temperature on the absorption spectrum of the hydrated electron and on its bimolecular recombination reaction//Journal of Physical Chemistry- 1967. Vol. 71, p. 2102−2106.
- R.K. Quinn, J.J. Lagowski, Metal-ammonia solutions. IV. spectra of dilute metal-ammonia solutions// Journal of Physical Chemistry- 1969.- Vol.73, p.2326−2329.
- J. Schnitker, P. J. Rossky, Quantum simulation study of the hydrated electron //Journal of Chemical Physics- March 1987.- Vol.86, № 6.- p. 3471−3485.
- D. Eisenberg, W. Kauzmann, The structure and properties of water. Oxford, London, 1969.
- L. Blum, A. J. Torruella, Invariant expansion for two-body correlations: Thermodynamic functions, scattering, and the Ornstein-Zernike equation// Journal of Chemical Physics- 1972.- Vol. 56, № 1.- p. 303−310.
- Q. H. Du, D. Beglov, B. Roux, Solvation free energy of polar and nonpolar molecules in water: An extended interaction site integral equation theory in three dimensions// Journal of Physical Chemistry B- February 2000.- Vol. 104, № 4.- p. 796−805.
- R. J. Baxter, Ornstein-Zernike relation and percus-yevick approximation for fluid mixtures// The Journal of Chemical Physics 1970. — Vol. 52, p. 45 594 562.
- S. Miura, F. Hirata, Temperature-dependence of the stability of a hydrated electron — an integral-equation study // Journal of Physical Chemistry-September 1994.- Vol.98, № 38.- p. 9649−9656.
- P. Graf, A. Nitzan, G. H. F. Diercksen, Phenomenology of electron solvation in polar fluids//Journal of Physical Chemistry- December 1996.- Vol. 100, № 49 p. 18 916−18 923.
- J. P. Perdew, A. Zunger, Self-interaction correction to density-functional approximations for many-electron systems//Physical Review B- 1981. Vol. 23, № 10 — p. 5048−5079.
- M. V. Fedorov, A. A. Kornyshev, Unravelling the solvent response to neutral and charged solutes//Molecular Physics- January 2007, — Vol. 105, № 1.- p. 1−16.
- L. R. Pratt, G. Hummer, Simulation of Electrostatic Interactions in solution. AIP, New York, 1999.
- R. Kubo, M. Toda, N. Hashitsume, Statistical Physics II. Springer, Berlin, 1995.
- J. Aqvist, T. Hansson, On the validity of electrostatic linear response in polar solvents//Journal of Physical Chemistry- May 1996.- Vol.100, № 22 p. 9512−9521.
- H. Reiss, Scaled particle methods in the statistical thermodynamics of fluids //Advanves in Chemical Physics- 1966.- Vol. 9, p. 1−84.
- S. J. Miyake, Strong-coupling limit of polaron ground-state// Journal of the Physical Society of Japan- 1975. Vol. 38, № 1.- p. 181−182.
- В.Я. Антонченко, А. С. Давыдов, В. В. Ильин, Основы физики воды. -Наукова Думка, Киев, 1991.
- L. D. Barron, L. Hecht, G. Wilson, The lubricant of life: A proposal that solvent water promotes extremely fast conformational fluctuations in mobile heteropolypeptide structure//Biochemistry- October 1997.- Vol.36, № 43-p. 13 143−13 147.
- A. Ben-Naim, Y. Marcus, Solvation thermodynamics of nonionic solutes // Journal of Chemical Physics- 1984.- Vol.81, № 4 p.2016−2027.
- Y. Marcus, Thermodynamics of solvation of ions. 5. gibbs free-energy of hydration at 298.15-K // Journal of the Chemical Society — Faraday Transactions- September 1991.- Vol.87, № 18 p. 2995−2999.
- M. А. Воротынцев, А. А. Корнышев, Электростатика сред с пространственной дисперсией. Наука, Москва, 1993.
- G. Hummer, L. R. Pratt, А. Е. Garcia, Free energy of ionic hydration// Journal of Physical Chemistry- January 1996.- Vol.100, № 4 p. 1206−1215.
- R. M. Lynden-Bell, J. C. Rasaiah, From hydrophobic to hydrophilic behaviour: A simulation study of solvation entropy and free energy of simple solutes // Journal of Chemical Physics- August 1997.- Vol. 107, № 6, — p. 1981−1991.
- S. H. Chong, F. Hirata, Ion hydration: Thermodynamic and structural analysis with an integral equation theory of liquids// Journal of Physical Chemistry В April 1997.- Vol. 101, № 16- p. 3209−3220.
- M. V. Vener, I. V. Leontyev, M. V. Basilevsky, Computations of solvation free energies for polyatomic ions in water in terms of a combined molecular-continuum approach//Journal of Chemical Physics- 2003.- Vol. 119, № 15-p.8038−8046.
- F. Hirata, editor Molecular theory of solvation. Kluwer Academic Publishers, Dordrecht, Netherlands, 2003.
- M. Salomon, Thermodynamics of ion solvation in water and propylene carbonate//Journal of Physical Chemistry- 1970.- Vol.74, № 12 p. 25 192 524.
- W. H. Robertson, M. A. Johnson, Molecular aspects of halide ion hydration: The cluster approach//Annual Review of Physical Chemistry- 2003.- Vol. 54, p. 173−213.
- P. Auffinger, L. Bielecki, E. Westhof, Anion binding to nucleic acids//Structure March 2004.- Vol. 12, № 3.- p. 379−388.
- A. Botti, F. Bruni, S. Imberti, M. A. Ricci, A. K. Soper, Ions in water: The microscopic structure of concentrated NaOH solutions // Journal of Chemical Physics- June 2004, — Vol. 120, № 21- p. 10 154−10 162.
- A. Botti, F. Bruni, S. Imberti, M. A. Ricci, A. K. Soper, Ions in water: The microscopic structure of a concentrated HC1 solution// Journal of Chemical Physics- October 2004.- Vol. 121, № 16 p. 7840−7848.
- A. A. Zavitsas, Aqueous solutions of calcium ions: Hydration numbers and the effect of temperature// Journal of Physical Chemistry B November 2005. -Vol. 109, № 43, — p. 20 636−20 640.
- T. M. Raschke, M. Levitt, Detailed hydration maps of benzene and cyclohexane reveal distinct water structures//Journal of Physical Chemistry B- September 2004.- Vol. 108, № 35.- p. 13 492−13 500.
- D. Spangberg, K. Hermansson, Many-body potentials for aqueous Li+, Na+, Mg2+, and A/3+: Comparison of effective three-body potentials and polarizable models// Journal of Chemical Physics- March 2004, — Vol.120, № 10- p. 4829−4843.
- M. Machuqueiro, A. M. Baptista, Constant-pH molecular dynamics with ionic strength effects: Protonation-conformation coupling in decalysine// Journal of Physical Chemistry B- February 2006.- Vol. 110, № 6 p. 2927−2933.
- R. Zangi, M. Hagen, B. J. Berne, Effect of ions on the hydrophobic interaction between two plates// Journal of the American Chemical Society- 2007.- Vol. 129, № 15 p. 4678−4686.
- J.-P. Hansen, I. R. McDonald, Theory of Simple Liquids, 3rd ed. Academic Press, London, 1991.
- B. M. Pettitt, P. J. Rossky, Integral-equation predictions of liquid-state structure for waterlike intermolecular potentials// Journal of Chemical Physics 1982.- Vol.77, № 3.- p. 1451−1457.
- F. O. Raineri, H. Resat, H. L. Friedman, Static longitudinal dielectric function of model molecular fluids// Journal of Chemical Physics- February 1992. — Vol.96, № 4.- p.3068−3084.
- H. A. Yu, B. M. Pettitt, M. Karplus, Aqueous solvation of n-methylacetamide conformers: Comparison of simulations and integral-equation theories// Journal of the American Chemical Society- March 1991.- Vol. 113, № 7.- p. 24 252 434.
- T. Fonseca, B. M. Ladanyi, Wave vector dependent static dielectric-properties of associated liquidsmethanol//Journal of Chemical Physics- December 1990.- Vol.93, № 11- p.8148−8155.
- C. Martin, M. Lombardero, M. Alvarez, E. Lomba, Atomic-structure factors from a molecular integral-equation theory: An application to homonuclear diatomic fluids//Journal of Chemical Physics- February 1995.- Vol.102, № 5 p. 2092−2097.
- M. Kinoshita, Y. Okamoto, F. Hirata, Calculation of solvation free energy using RISM theory for peptide in salt solution // Journal of Computational Chemistry- November 1998.- Vol. 19, № 15 p. 1724−1735.
- T. Imai, M. Kinoshita, F. Hirata, Salt effect on stability and solvation structure of peptide: An integral equation study // Bulletin of the Chemical Society of Japan- May 2000.- Vol.73, № 5 p. 1113−1122.
- A. Kovalenko, F. Hirata, Potential of mean force between two molecular ions in a polar molecular solvent: A study by the three-dimensional reference interaction site model//Journal of Physical Chemistry B- 1999.- Vol. 103, p.7942−7957.
- A. Kovalenko, F. Hirata, Self-consistent description of a metal-water interface by the kohn-sham density functional theory and the three-dimensional reference interaction site model// Journal of Chemical Physics- 1999.- Vol. 110, p.10 095−10 112.
- D. Chandler, Dielectric-constant and related equilibrium properties of molecular fluidsinteraction site cluster theory analysis // Journal of Chemical Physics- 1977.- Vol.67, № 3.- p. 1113−1124.
- F. Hirata, B. M. Pettitt, P. J. Rossky, Application of an extended RISM equation to dipolar and quadrupolar fluids // Journal of Chemical Physics -1982.- Vol.77, № 1.- p.509−520.
- C. M. Cortis, P. J. Rossky, R. A. Friesner, A three-dimensional reduction of the ornstein-zernicke equation for molecular liquids//Journal of Chemical Physics- 1997. Vol. 107, p. 6400−6414.
- G. N. Chuev, S. Chiodo, S. E. Erofeeva, M. V. Fedorov, N. Russo, E. Sicilia, A quasilinear RISM approach for the computation of solvation free energy ofionic species//Chemical Physics Letters- February 2006.- Vol.418, № 4−6-p. 485−489.
- A. Kovalenko, T. N. Truong, Thermochemistry of solvation: A self-consistent three-dimensional reference interaction site model approach // Journal of Chemical Physics- November 2000.- Vol. 113, № 17 p. 7458−7470.
- A. Kovalenko, F. Hirata, Hydration free energy of hydrophobic solutes studied by a reference interaction site model with a repulsive bridge correction and a thermodynamic perturbation method//Journal of Chemical Physics- 2000.-Vol. 113, p. 2793−2805.
- J. G. Kirkwood, Statistical mechanics of fluid mixtures//Journal of Chemical Physics- 1935.- Vol. 3, p. 300−313.
- P. T. Cummings, G. Stell, Exact asymptotic form of the site-site direct correlation-function for rigid polar-molecules// Molecular Physics- 1981.-Vol.44, № 2, — p. 529−531.
- P. J. Rossky, B. M. Pettitt, G. Stell, The coupling of long and short-range correlations in ISM liquids//Molecular Physics- 1983.- Vol.50, № 6 p. 1263−1271.
- A. D. Trokhymchuk, M. F. Holovko, K. Heinzinger, Static dielectric-properties of a flexible water model// Journal of Chemical Physics- August 1993. Vol. 99, № 4 — p. 2964−2971.
- F. O. Raineri, G. Stell, Dielectrically nontrivial closures for the RISM integral equation//Journal of Physical Chemistry B- November 2001.- Vol.105, № 47.- p. 11 880−11 892.
- S. Chiodo, G. N. Chuev, S. E. Erofeeva, M. V. Fedorov, N. Russo, E. Sicilia, Comparative study of electrostatic solvent response by rism and pcm methods //International Journal of Quantum Chemistry- 2006. Vol. 107, p. 265−274.
- B. H. Besler, K. M. Merz, P. A. Kollman, Atomic charges derived from semiempirical methods// Journal of Computational Chemistry- May 1990.- Vol.11, № 4- p. 431−439.
- J. R. Pliego, J. M. Riveros, Gibbs energy of solvation of organic ions in aqueous and dimethyl sulfoxide solutions // Physical Chemistry Chemical Physics -2002, — Vol.4, p. 1622−1627.
- B. E. Conway, Ionic Hydration in Chemistry and Biophysics. Elsevier, Amsterdam, 1981.
- Yizhak Marcus, Ion solvation. John Wiley & Sons, Chichester, UK, 1985.
- R. R. Dogonadze, E. Kalman, A. A. Kornyshev, J. Ulstrup, editors The Chemical Physics of Solvation. Part A. Elsevier, Amsterdam, 1985.
- R. R. Dogonadze, E. Kalman, A. A. Kornyshev, J. Ulstrup, editors The Chemical Physics of Solvation. Part B. Elsevier, Amsterdam, 1986.
- P. A. Bopp, A. A. Kornyshev, G. Sutmann, Static nonlocal dielectric function of liquid water//Physical Review Letters- February 1996.- Vol.76, № 8 p. 1280−1283.
- A. P. Lyubartsev, A. Laaksonen, Concentration effects in aqueous nacl solutions, a molecular dynamics simulation//Journal of Physical Chemistry-October 199G. Vol. 100, № 40, — p. 16 410−16 418.
- G. Hummer, L. R. Pratt, A. E. Garcia, Multistate gaussian model for electrostatic solvation free energies// Journal of the American Chemical Society- September 1997.- Vol. 119, № 36.- p. 8523−8527.
- P. A. Bopp, A. A. Kornyshev, G. Sutmann, Frequency and wave-vector dependent dielectric function of water: Collective modes and relaxation spectral// Journal of Chemical Physics- August 1998.- Vol.109, № 5 p. 1939−1958.
- D. M. Huang, P. L. Geissler, D. Chandler, Scaling of hydrophobic solvation free energies//Journal of Physical Chemistry B- July 2001.- Vol. 105, № 28-p.6704−6709.
- J. Dzubiella, J. P. Hansen, Reduction of the hydrophobic attraction between charged solutes in water//Journal of Chemical Physics- December 2003.-Vol. 119, № 23.- p. 12 049−12 052.
- Y. Laudernet, T. Cartailler, P. Turq, M. Ferrario, A microscopic description of concentrated potassium fluoride aqueous solutions by molecular dynamics simulation//Journal of Physical Chemistry B- March 2003. Vol. 107, № 10-p.2354−2361.
- J. Dzubiella, J. P. Hansen, Competition of hydrophobic and coulombic interactions between nanosized solutes // Journal of Chemical Physics-September 2004.- Vol. 121, № 11- p. 5514−5530.
- F. Bresme, Integral equations and simulation studies of waterlike models// Journal of Chemical Physics- March 1998.- Vol. 108, № 11- p. 4505−4515.
- R. R. Dogonadze, A. A. Kornyshev, Polar-solvent structure in theory of ionic solvation// Journal of the Chemical Society — Faraday Transactions II- 1974. Vol.70, № 7 — p. 1121−1132.
- A. A. Kornyshev, Non-local dielectric response of a polar-solvent and debye-screening in ionic solution // Journal of the Chemical Society — Faraday Transactions II- 1983.- Vol.79, p.651−661.
- A. A. Kornyshev In R.R. Dogonadze, E. Kalman, A.A. Kornyshev, J. Ulstrup, editors, The Chemical Physics of Solvation. Part A page p.77. Elsevier, Amsterdam 1985.
- M. V. Basilevsky, D. F. Parsons, Nonlocal continuum solvation model with exponential susceptibility kernels//Journal of Chemical Physics- 1998.- Vol. 108, № 21- p. 9107−9113.
- J. Liszi, I Ruff In R.R. Dogonadze, E. Kalman, A.A. Kornyshev, J. Ulstrup, editors, The Chemical Physics of Solvation. Part A page 119. Elsevier, Amsterdam 1985.
- Y. Hatano, T. Kakitani, A. Yoshimori, M. Saito, N. Mataga, Theoretical study of dielectric saturation in molecular solutions by the monte carlo simulation// Journal of the Physical Society of Japan- 1990.- Vol. 59, № 3.- p. 1104−1116.
- A. A. Kornyshev, G. Sutmann, Nonlocal dielectric saturation in liquid water //Physical Review Letters- November 1997.- Vol.79, № 18 p.3435−3438.
- A. A. Kornyshev, G. Sutmann, Nonlocal nonlinear static dielectric response of polar liquids// Journal of Electroanalytical Chemistry- June 1998.- Vol. 450, № 1- p. 143−156.
- A. Geiger, Molecular-dynamics simulation study of the negative hydration effect in aqueous-electrolyte solutions // Berichte der Bunsen-Gesellschaft-Physical Chemistry Chemical Physics- 1981.- Vol.85, № 1- p.52−63.
- M. N. Buslaeva, 0. Ya. Samoilov In R.R. Dogonadze, E. Kalman, A.A. Kornyshev, J. Ulstrup, editors, The Chemical Physics of Solvation. Part A page p.391. Elsevier, Amsterdam 1985.
- J-Y. Huot, C. Jolicoer In R.R. Dogonadze, E. Kalman, A.A. Kornyshev, J. Ulstrup, editors, The Chemical Physics of Solvation. Part A page 417. Elsevier, Amsterdam 1985.
- A. A. Kornyshev, G. Sutmann, Nonlocal dielectric function of water: How strong are the effects of intramolecular charge form factors? // Journal of Molecular Liquids- September 1999, — Vol.82, № 1−2 p. 151−160.
- R. F. W. Bader, G. A. Jones, The electron density distributions in hydride molecules, i, the water molecule// Canadian Journal of Chemistry- 1963. — Vol. 41, p. 586−606.
- J. W. Caldwell, P. A. Kollman, Structure and properties of neat liquids using nonadditive molecular-dynamicswater, methanol, and n-methylacetamide // Journal of Physical Chemistry- April 1995, — Vol.99, № 16 p.6208−6219.
- S. Walbran, A. A. Kornyshev, Proton transport in polarizable water//Journal of Chemical Physics- June 2001.- Vol. 114, № 22 p. 10 039−10 048.
- E. Harder, J. D. Eaves, A. Tokmakoff, B. J. Berne, Polarizable molecules in the vibrational spectroscopy of water//Proceedings of the National Academy of Sciences of the United States of America- August 2005, — Vol. 102, № 33-p. 11 611−11 616.
- E. Spohr, P. Commer, A. A. Kornyshev, Enhancing proton mobility in polymer electrolyte membranes: Lessons from molecular dynamics simulations// Journal of Physical Chemistry B- October 2002.- Vol. 106, № 41.- p. 10 560−10 569.
- A. A. Kornyshev, A. M. Kuznetsov, E. Spohr, J. Ulstrup, Kinetics of proton transport in water//Journal of Physical Chemistry B April 2003. — Vol. 107, № 15.- p. 3351−3366.
- L. Lue, D. Blankschtein, Application of integral-equation theories to predict the structure, thermodynamics, and phase-behavior of water // Journal of Chemical Physics- April 1995.- Vol. 102, № 13.- p. 5427−5437.
- M. Born,//Zeitschrift fuer Physik- 1920.- Vol. 1, p. 45.
- W. R. Fawcett, Thermodynamic parameters for the solvation of monatomic ions in water// Journal of Physical Chemistry B- December 1999.- Vol. 103, № 50 p. 11 181−11 185.
- A. A. Kornyshev, D. A. Kossakowski, M. A. Vorotyntsev In M. P. Tosi, A. A. Kornyshev, editors, Condensed Matter Physics Aspects of Electrochemistry page p.92. World Scientific, Singapore 1991.
- S. I. Mamatkulov, P. K. Khabibullaev, R. R. Netz, Water at hydrophobic substrates: Curvature, pressure, and temperature effects//Langmuir- May 2004.- Vol.20, № 11.- p.4756−4763.
- К. А. Тау, F. Bresme, Wetting properties of passivated metal nanocrystals at liquid-vapor interfaces: A computer simulation study// Journal of the American Chemical Society- November 2006.- Vol. 128, № 43.- p. 14 166−14 175.
- G. Hummer, S. Garde, A. E. Garcia, M. E. Paulaitis, L. R. Pratt, Hydrophobic effects on a molecular scale // Journal of Physical Chemistry В December 1998.- Vol. 102, № 51- p. 10 469−10 482.
- P. Jedlovsky, M. Predota, I. Nezbeda, Hydration of apolar solutes of varying size: A systematic study//Molecular Physics- August 2006. Vol. 104, № 15-p.2465−2476.
- M. P. Krafft, Fluorocarbons and fluorinated amphiphiles in drug delivery and biomedical research//Advanced Drug Delivery Reviews- 2001.- Vol.47, p. 209−228.
- Г. P. Иваницкий, Биофизика на пороге нового тысячелетия: Перфторугле-родные среды и газотранспортные кровезаменители//Биофизика- 2001. Vol. 46, р. 5−33.
- Б. В. Дерягин, Н. В. Чураев, В. М. Муллер, Поверхностные силы. Наука, Москва, 1985.
- Yethiraj A Schweizer Ks, Polymer reference interaction site model-theory — new molecular closures for phase-separating fluids and alloys// Journal of Chemical Physics- 1993.- Vol.98, № 11.- p.9053−9079.
- A. Reddy, The behavior of fluids near solutes: A density functional theory and computer simulation study// Journal of Chemical Physics- 2004.- Vol. 121, № 9 p. 4203−4209.
- P. U. Kenkare, С. K. Hall, P. K. Kilpatrick, The effects of salts on the lower consolute boundary of a nonionic micellar solution // Journal of Colloid and Interface Science- 1996.- Vol. 184, p. 456−468.
- R. W. Chang, A. Yethiraj, Brownian dynamics simulations of salt-free polyelectrolyte solutions//Journal of Chemical Physics- March 2002.- Vol. 116, № 12.- p. 5284−5298.
- H. H. Griinberg, R. Klein, Density functional theory of nonuniform colloidal suspensions: 3D density distributions and depletion forces // The Journal of Chemical Physics- 1999.- Vol. 110, p. 5421−5431.
- M. Schmidt, Density functional theory for colloidal rod-sphere mixtures // Physical Review E- 2001.- Vol.63, p. 50 201.
- C. Y. Shew, A. Yethiraj, Integral equation theory for the structure of DNA solutions// Journal of Chemical Physics- March 2002.- Vol. 116, № 12- p. 5308−5314.
- A. Yethiraj, A. van Blaaderen, A colloidal model system with an interaction tunable from hard sphere to soft and dipolar//Nature- January 2003.- Vol. 421, № 6922, — p. 513−517.
- C. K. Smith, L. Regan, Construction and design of beta-sheets// Accounts of Chemical Research- April 1997.- Vol.30, № 4 p. 153−161.
- D. M. Mariiii, W. Hwang, D. A. Lauffenburger, S. G. Zhang, R. D. Kamm, Left-handed helical ribbon intermediates in the self-assembly of a /?-sheet peptide//Nano Letters- April 2002.- Vol.2, № 4 p. 295−299.
- W. M. Hwang, D. M. Marini, R. D. Kamm, S. Q. Zhang, Supramolecular structure of helical ribbonsself-assembled from a /3-sheet peptide // Journal of Chemical Physics- 2003.- Vol. 118, p. 389−397.
- D. G. Lynn, S. C. Meredith, Review: Model peptides and the physicochemical approach to beta-amyloids// Journal of Structural Biology- June 2000. Vol. 130, № 2−3 — p. 153−173.
- C. Chothia, Conformation of twisted beta-pleated sheets in proteins// Journal of Molecular Biology- 1973.- Vol.75, № 2.- p. 295−302.
- J. S. Richardson, The anatomy and taxonomy of protein structure.//Advanced Protein Chemistry- 1981.- Vol. 34, p. 167−339.
- D. W. Weatherford, F. R. Salemme, Conformations of twisted parallel /3-sheets and the origin of chirality in protein structures//Proceedings of the National Academy of Sciences of the United States of America- 1979. Vol. 76, № 1-p.19−23.
- F. R. Salemme, Structural-properties of protein /3-sheets // Progress in Biophysics and Molecular Biology- 1983.- Vol.42, № 2−3.- p. 95−133.
- A. S. Yang, B. Honig, Free-energy determinants of secondary structure formation. 2. antiparallel /3-sheets// Journal of Molecular Biology- September 1995.- Vol.252, № 3.- p.366−376.
- L. Wang, T. OConnell, A. Tropsha, J. Hermans, Molecular simulations of /3-sheet twisting// Journal of Molecular Biology- September 1996.- Vol.262, № 2, — p. 283−293.
- I. L. Shamovsky, G. M. Ross, R. J. Riopelle, Theoretical studies on the origin of /3-sheet twisting// Journal of Physical Chemistry B November 2000. — Vol.104, № 47- p. 11 296−11 307.
- B. K. Ho, P. M. G. Curmi, Twist and shear in /3-sheets and beta-ribbons// Journal of Molecular Biology- March 2002.- Vol.317, № 2.- p.291−308.
- J. V. Selinger, M. S. Spector, J. M. Schnur, Theory of self-assembled tubules and helical ribbons//Journal of Physical Chemistry B- August 2001.- Vol.105, № 30 p. 7157−7169.
- G. Bellesia, M. V. Fedorov, Y. A. Kuznetsov, E. G. Timoshenko, Structure and stability of chiral beta-tapes: A computational coarse-grained approach// Journal of Chemical Physics- April 2005.- Vol. 122, № 13 p. 134 901.
- D. A. C. Beck, R. S. Armen, V. Daggett, Cutoff size need not strongly influence molecular dynamics results for solvated polypeptides//Biochemistry- January 2005.- Vol.44, № 2.- p.609−616.
- A. Baumketner, J. E. Shea, The influence of different treatments of electrostatic interactions on the thermodynamics of folding of peptides //
- Journal of Physical Chemistry B- November 2005.- Vol.109, № 45 p. 21 322−21 328.
- R. D. Lins, U. Rothlisberger, Influence of long-range electrostatic treatments on the folding of the n-terminal h4 histone tail peptide// Journal of Chemical Theory and Computation- 2006, — Vol.2, № 2 p.246−250.
- C. Sagui, T. A. Darden, Molecular dynamics simulations of biomolecules: Long-range electrostatic effects // Annual Review of Biophysics and Biomolecular Structure- 1999.- Vol.28, p. 155−179.
- Hyperchem™, hypercube, inc., 1115 nw 4th street, gainesville, florida 32 601, usa.
- J. C. Phillips, R. Braun, W. Wang, J. Gumbart, E. Tajkhorshid, E. Villa, C. Chipot, R. D. Skeel, L. Kale, K. Schulten, Scalable molecular dynamics with NAMD// Journal of Computational Chemistry- December 2005.- Vol. 26, № 16, — p. 1781−1802.
- W. Humphrey, A. Dalke, K. Schulten, VMD: Visual molecular dynamics// Journal of Molecular Graphics- February 1996.- Vol. 14, № 1- p. 33−38.
- H. C. Andersen, Rattle — a velocity version of the shake algorithm for molecular-dynamics calculations// Journal of Computational Physics- 1983.- Vol.52, № 1, — p.24−34.
- H. J. C. Berendsen, J. P. M. Postma, W. F. van Gunsteren, A. Dinola, J. R. Haak, Molecular-dynamics with coupling to an external bath // Journal of Chemical Physics- 1984.- Vol.81, № 8.- p.3684−3690.
- R. Garemyr, A. Elofsson, Study of the electrostatics treatment in molecular dynamics simulations // Proteins: Structure, Function, and Genetics-November 1999.- Vol.37, № 3.- p.417−428.
- W. Kabsch, Solution for best rotation to relate 2 sets of vectors // Acta Crystallographica Section A- 1976.- Vol.32, p.922−923.
- W. Kabsch, Discussion of solution for best rotation to relate 2 sets of vectors //Acta Crystallographica Section A- 1978.- Vol. 34, p. 827−828.
- H. J. C. Berendsen, D. Spoel, R. Drunen, Gromacs: A message-passing parallel molecular dynamics implementation// Computer Physics Communications-1995. Vol. 91, p. 43−56.
- E. Lindahl, B. Hess, D. van der Spoel, GROMACS 3.0: A package for molecular simulation and trajectory analysis// Journal of Molecular Modeling- 2001. — Vol. 7, p. 306−317.
- Pdb files of the representative structures are available on request.
- P.R. Bergethon, The Physical Basis of Biochemistry: The Foundations of Molecular Biophysics. Springer, New York, 1998.
- S. Hovmoller, T. Zhou, T. Ohlson, Conformations of amino acids in proteins // Acta Crystallographica Section D: Biological Crystallography- May 2002. Vol. 58, p. 768−776.
- B. J. Stapley, T. P Creamer, A survey of left-handed polyproline II helices// Protein Science- March 1999.- Vol.8, № 3.- p.587−595.
- C. Branden, J. Tooze, Introduction to Protein Structure. Garland Publishing Inc., New York, 1999.
- G.N. Ramachandran, C. Ramakrishnan, V. Sasisekharan, Stereochemistry of polypeptide chain configurations//Journal of Molecular Biology- 1963.- Vol. 7, p.95−99.
- G.N. Ramachandran, V. Sasisekharan, Conformation of polypeptides and proteins//Advances in Protein Chemistry- 1968.- Vol. 23, p. 283−438.
- R.B. Corey, L. Pauling, Fundamental dimensions of polypeptide chains// Proc R Soc Lond B Biol Sci.- 1953.- Vol. 141(902), p. 10−20.
- A. B. Harris, R. D. Kamien, T. C. Lubensky, Molecular chirality and chiral parameters//Reviews of Modern Physics- October 1999, — Vol.71, № 5, — p. 1745−1757.
- A. A. Kornyshev, S. Leikin, Theory of interaction between helical molecules //Journal of Chemical Physics- September 1997, — Vol. 107, № 9- p.3656−3674.
- A. A. Kornyshev, S. Leikin, Theory of interaction between helical molecules// Journal of Chemical Physics- April 1998.- Vol. 108, № 16 p. 7035−7035.
- A. A. Kornyshev, S. Leikin, Electrostatic interaction between long, rigid helical macromolecules at all interaxial angles//Physical Review E- August 2000.-Vol. 62, № 2.- p. 2576−2596.
- A. A. Kornyshev, S. Leikin, Twist in chiral interaction between biological helices// Physical Review Letters- March 2000.- Vol.84, № 11- p. 25 372 540.
- N. Nandi, B. Bagchi, Prediction of the senses of helical amphiphilic assemblies from effective intermolecular pair potential: Studies on chiral monolayers and bilayers// Journal of Physical Chemistry A- February 1997.- Vol. 101, № 7-p.1343−1351.
- A. Mukherjee, B. Bagchi, Correlation between rate of folding, energy landscape, and topology in the folding of a model protein HP-36 // Journal of Chemical Physics- March 2003.- Vol. 118, № 10 p. 4733−4747.
- N. Metropolis, A.W. Rosenbluth, M.N. Rosenbluth, A.H. Teller, E. Teller, Equation of state calculations by fast computing machines // The Journal of Chemical Physics- 1953.- Vol.21, p. 1087−1092.
- D.J. Struik, Lectures on Classical Differential Geometry. Dover, New York, 1988.
- M. Levitt, A. Warshel, Computer simulation of protein folding//Nature 1975. — Vol. 253, p. 694−698.
- M. Levitt, Simplified representation of protein conformations for rapid simulation of protein folding// Journal of Molecular Biology- 1976.- Vol. 104, № 1- p. 59−107.
- J. D. Honeycutt, D. Thirumalai, The nature of folded states of globular-proteins//Biopolymers- June 1992.- Vol.32, № 6 p.695−709.
- J. D. Honeycutt, D. Thirumalai, Metastability of the folded states of globular-proteins // Proceedings of the National Academy of Sciences of the United States of America- May 1990.- Vol.87, № 9- p. 3526−3529.
- S. Takada, Z. Luthey-Schulten, P. G. Wolynes, Folding dynamics with nonadditive forces: A simulation study of a designed helical protein and a random heteropolymer//Journal of Chemical Physics- June 1999.- Vol. 110, № 23.- p. 11 616−11 629.
- M. S. Cheung, J. M. Finke, B. Callahan, J. N. Onuchic, Exploring the interplay between topology and secondary structural formation in the protein folding problem//Journal of Physical Chemistry B- October 2003.- Vol. 107, № 40-p.11 193−11 200.
- M. S. Cheung, L. L. Chavez, J. N. Onuchic, The energy landscape for protein folding and possible connections to function// Polymer January 2004. — Vol. 45, № 2 — p. 547−555.
- D. K. Klimov, M. R. Betancourt, D. Thirumalai, Virtual atom representation of hydrogen bonds in minimal off-lattice models of alpha helices: Effect on stability, cooperativity and kinetics//Folding and Design- 1998.- Vol.3, № 6.- p. 481−496.
- A. Baumketner, Y. Hiwatari, Diffusive dynamics of protein folding studied by molecular dynamics simulations of an off-lattice model// Physical Review E -July 2002.- Vol.66, № 1- p.11 905.
- H. Yamakawa, Helical Wormlike Chains in Polymer Solutions. Springer, Berlin, 1997.
- C. Bonnet-Gonnet, S. Leikin, S. Chi, D. C. Rau, V. A. Parsegian, Measurement of forces between hydroxypropylcellulose polymers: Temperature favored assembly and salt exclusion//Journal of Physical Chemistry B- March 2001. Vol. 105, № 9.- p. 1877−1886.
- A. G. Cherstvy, A. A. Kornyshev, S. Leikin, Temperature-dependent DNA condensation triggered by rearrangement of adsorbed cations // Journal of Physical Chemistry B- December 2002.- Vol. 106, № 51- p. 13 362−13 369.
- L. C. Serpell, M. Sunde, C. C. F. Blake, The molecular basis of amyloidosis //Cellular and Molecular Life Sciences- December 1997.- Vol.53, № 11−12-p. 871−887.
- M. Boncheva, D. A. Bruzewicz, G. M. Whitesides, Formation of chiral, three-dimensional aggregates by self-assembly of helical components//Langmuir-July 2003.- Vol. 19, № 15.- p. 6066-G071.
- K. Lu, J. Jacob, P. Thiyagarajan, V. P. Conticello, D. G. Lynn, Exploiting amyloid fibril lamination for nanotube self-assembly//Journal of the American Chemical Society- May 2003.- Vol. 125, № 21- p. 6391−6393.
- E. Barry, Z. Hensel, Z. Dogic, M. Shribak, R. Oldenbourg, Entropy-driven formation of a chiral liquid-crystalline phase of helical filaments // Physical Review Letters- January 2006.- Vol.96, № 1- p.18 305.
- J. P. Straley, Theory of piezoelectricity in nematic liquid-crystals, and of cholesteric ordering//Physical Review A- 1976.- Vol. 14, № 5 p. 1835−1841.
- R. L. B. Selinger, J. V. Selinger, A. R Malanoski, J. M. Schnur, Shape selection in chiral self-assembly // Physical Review Letters October 2004. — Vol. 93, № 15- p. 158 103.
- R. Ghafouri, R. Bruinsma, Helicoid to spiral ribbon transition // Physical Review Letters- April 2005.- Vol.94, № 13 p. 138 101.
- G. Bellesia, M. V. Fedorov, E. G. Timoshenko, Molecular dynamics study of structural properties of ?3-sheet assemblies formed by synthetic de novo oligopeptides//Physica A-Statistical Mechanics and its Applications January 2007.- Vol.373, p.455−476.
- Weisstein — http://mathworld.wolfram.com/circularsector.html.
- I. A. Nyrkova, A. N. Semenov, A. Aggeli, N. Boden, Fibril stability in solutions of twisted /5-sheet peptides: A new kind of micellization in chiral systems // European Physical Journal B- October 2000.- Vol. 17, № 3 p. 481−497.
- M. Doi, S. F. Edwards, The Theory of Polymer Dynamics. Oxford University Press Inc., New York, 1998.
- N. C. Price, R. A. Dwek, M. Wormald, G. R. Ratcliffe, Principles and problems in physical chemistry for biochemists. Oxford University press, 2001.
- R. L. Baldwin, How hofmeister ion interactions affect protein stability // Biophysical Journal- October 1996.- Vol. 71, № 4 p. 2056−2063.
- S. A. Hassan, Amino acid side chain interactions in the presence of salts //Journal of Physical Chemistry B- November 2005.- Vol.109, № 46 p. 21 989−21 996.
- T. Ghosh, A. Kalra, S. Garde, On the salt-induced stabilization of pair and many-body hydrophobic interactions // Journal of Physical Chemistry B -January 2005.- Vol. 109, № 1, — p. 642−651.
- T. Arakawa, S. N. Timasheff, Abnormal solubility behavior of beta-lactoglobulin salting-in by glycine and NaCl//Biochemistry August 1987. — Vol. 26, № 16 — p. 5147−5153.
- Y. Goto, N. Takahashi, A. L. Fink, Mechanism of acid-induced folding of proteins//Biochemistry- 1990.- Vol.29, p.3480−3488.
- Y. Goto, S. Aimoto, Anion and pH-dependent conformational transition of an amphiphilic polypeptide// Journal of Molecular Biology- March 1991. Vol. 218, № 2 — p. 387−396.
- Y. Goto, Y. Hagihara, Mechanism of the conformational transition of melittin //Biochemistry- January 1992.- Vol.31, № 3 p.732−738.
- R. A. Curtis, J. M. Prausnitz, H. W. Blanch, Protein-protein and protein-salt interactions in aqueous protein solutions containing concentrated electrolytes// Biotechnology and Bioengineering- January 1998.- Vol.57, № 1- p. 11−21.
- R. A. Curtis, J. Ulrich, A. Montaser, J. M. Prausnitz, H. W. Blanch, Proteinprotein interactions in concentrated electrolyte solutions Hofmeister-series effects//Biotechnology and Bioengineering- August 2002.- Vol.79, № 4 — p. 367−380.
- J. J. McManus, J. O. Radler, K. A. Dawson, Does calcium turn a zwitterionic lipid cationic?// Journal of Physical Chemistry B- September 2003.- Vol. 107, № 36.- p. 9869−9875.
- J. J. McManus, J. O. Radler, K. A. Dawson, Observation of a rectangular columnar phase in a DNA-calcium-zwitterionic lipid complex // Journal of the American Chemical Society- December 2004. Vol. 126, № 49 — p. 1 596 615 967.
- M. G. Cacace, E. M. Landau, J. J. Ramsden, The hofmeister series: Salt and solvent effects on interfacial phenomena// Quarterly Reviews of Biophysics-August 1997.- Vol.30, № 3 p.241−277.
- G. Karlstrom, Oil the effective interaction between an ion and a hydrophobic particle in polar solvents, a step towards an understanding of the hofmeister effect?//Physical Chemistry Chemical Physics- 2003.- Vol.5, № 15-p. 3238−3246.
- S. N. Timasheff, Protein hydration, thermodynamic binding, and preferential hydration//Biochemistry- November 2002.- Vol.41, № 46- p. 13 473−13 482.
- M. J. Blandamer, J. B. F. N. Engberts, P. T. Gleeson, J. C. R. Reis, Activity of water in aqueous systems- a frequently neglected property.// Chemical Society Reviews- 2005.- Vol.2005, p.440−458.
- K. Zero, B. R. Ware, Mobilities of poly-l-lysine molecules in low-salt solutions //Journal of Chemical Physics- 1984.- Vol.80, № 4.- p. 1610−1616.
- G. Mezo, J. Kajtar, I. Nagy, M. Szekerke, F. Hudecz, Carrier design: Synthesis and conformational studies of poly (l-lysine) based branched polypeptides with hydroxyl groups in the side chains//Biopolymers- November 1997.- Vol. 42, № 6 p. 719−730.
- T. Segura, L. D. Shea, Materials for non-viral gene delivery//Annual Review of Materials Research- 2001.- Vol.31, p. 25−46.
- Y. L. Wang, Y. C. Chang, Synthesis and conformational transition of surface-tethered polypeptide: Poly (1-lysine) // Macromolecules August 2003. — Vol. 36, № 17 — p. 6511−6518.
- S. W. Rick, A reoptimization of the five-site water potential (TIP5P) for use with ewald sums//Journal of Chemical Physics- April 2004. Vol. 120, № 13-p.6085−6093.
- M. W. Mahoney, W. L. Jorgensen, A five-site model for liquid water and the reproduction of the density anomaly by rigid, nonpolarizable potential functions//Journal of Chemical Physics- May 2000.- Vol.112, № 20 p. 8910−8922.
- G. Schaftenaar, J. H. Noordik, Molden: A pre- and post-processing program for molecular and electronic structures// Journal of Computer-Aided Molecular Design- 2000.- Vol. 14, p. 123−134.
- Y. G. Mu, D. S. Kosov, G. Stock, Conformational dynamics of trialanine in water. 2. comparison of AMBER, CHARMM, GROMOS, and OPLS force fields to NMR and infrared experiments// Journal of Physical Chemistry B -May 2003.- Vol. 107, № 21- p. 5064−5073.
- M. V. Fedorov, S. Schumm, J. M. Goodman, Solvent effects and conformational stability of a tripeptide // Lecture Notes in Biolnformatics -2006.- Vol.4216, p. 141−149.
- S. Woutersen, P. Hamm, Structure determination of trialanine in water using polarization sensitive two-dimensional vibrational spectroscopy // Journal of Physical Chemistry B- Nov 2000.- Vol. 104, № 47 p. 11 316−11 320.
- S. Woutersen, P. Hamm, Isotope-edited two-dimensional vibrational spectroscopy of trialanine in aqueous solution// Journal of Chemical Physics -Feb 2001.- Vol. 114, № 6.- p. 2727−2737.
- R. Schweitzer-Stenner, F. Eker, Q. Huang, K. Griebenow, Dihedral angles of trialanine in D^O determined by combining FTIR and polarized visible raman spectroscopy// Journal of the American Chemical Society- October 2001.-Vol. 123, № 39 p. 9628−9633.
- D. van der Spoel, E. Lindahl, Brute-force molecular dynamics simulations of villin headpiece: Comparison with NMR parameters // Journal of Physical Chemistry B- October 2003.- Vol. 107, № 40 p. 11 178−11 187.441. http://www.octave.org/.
- A. Kalra, N. Tugcu, S. M. Cramer, S. Garde, Salting-in and salting-out of hydrophobic solutes in aqueous salt solutions// Journal of Physical Chemistry B- 2001.- Vol.105, № 27.- p. 6380−6386.
- S. Pal, F. Muller-Plathe, Molecular dynamics simulation of aqueous NaF and Nal solutions near a hydrophobic surface// Journal of Physical Chemistry B2005.- Vol. 109, № 13.- p. 6405−6415.
- R. Zangi, B. J. Berne, Aggregation and dispersion of small hydrophobic particles in aqueous electrolyte solutions// Journal of Physical Chemistry B2006.- Vol.110, № 45 p. 22 736−22 741.
- S. Bandyopadhyay, S. Chakraborty, B. Bagchi, Secondary structure sensitivity of hydrogen bond lifetime dynamics in the protein hydration layer// Journal of the American Chemical Society- November 2005. Vol. 127, № 47 — p. 1 666 016 667.
- D. Russo, R. K. Murarka, G. Hura, E. Verschell, J. R. A. Copley, T. Head-Gordon, Evidence for anomalous hydration dynamics near a model hydrophobic peptide// Journal of Physical Chemistry B December 2004. -Vol. 108, № 51- p. 19 885−19 893.
- D. Russo, R. K. Murarka, J. R. D. Copley, T. Head-Gordon, Molecular view of water dynamics near model peptides // Journal of Physical Chemistry B -July 2005. Vol. 109, № 26.- p. 12 966−12 975.