Thursday, January 09, 2014

Software Used in Molecular Modeling and Molecular Dynamics


Software Used in Molecular Modeling and Molecular Dynamics
bulletAMBER (UNIX; proprietary) at Peter A. Kollman's research group at the University of California San Francisco (Updated 5/22/99).
bulletDescription: AMBER refers to two things: a molecular mechanical force field for the simulation of biomolecules (which is in general use in a variety of simulation programs); and a package of molecular simulation programs which includes source code and demos.(Updated 5/22/99).
bulletAMMP (Unix, Linux, and PC; Free Downloadable Software) is a modern full-featured molecular mechanics, dynamics and modeling program. It can manipulate both small molecules and macromolecules including proteins, nucleic acids and other polymers. This software is found at Structural Biology at Jefferson and the Kimmel Cancer Center (Updated 5/22/99).
bulletCHARMM Homepage (UNIX; License Required) by Martin Karplus's group at Harvard University. Charmm has been integrated into the popular molecular modeling software package, QUANTA, of Molecular Simulations Inc. (MSI)(Updated 5/22/99)
bulletCHARMM Commands 
bulletDescription: CHARMm combines standard minimization and dynamics capabilities with expert features including free energy perturbation (FEP), correlation analysis and combined quantum and molecular mechanics (QM/MM) methods. Simulations provide insight into molecular-level structure, interactions, and energetics (Updatd 5/22/99).
bulletChem2Pac ( Windows, Free )is intended to be a kind of computational chemistry integrator, which has a multiple document interface, a molecular rendering utility, and allows the manipulation of various files (Updated 7/14/99).
bulletmore information
bullet Dalton Quantum Chemistry Programnew.GIF (Unix and Windows; Free, but License Required)(represents a powerful quantum chemistry program for the calculation of molecular properties with SCF, MP2 or MCSCF wave functions. The strengths of the program are mainly in the areas of magnetic and (frequency-dependent) electric properties, and for studies of molecular potential energy surfaces, both for static and dynamical investigations (Updated 7/14/99).
bulletDeep Viewer  new.GIF(free for PC and Macintosh) is an application that provides a user friendly interface allowing to analyse several proteins at the same time. The proteins can be superimposed in order to deduce structural alignments and compare their active sites or any other relevant parts. Amino acid mutations, H-bonds, angles and distances between atoms are easy to obtain thanks to the intuitive graphic and menu interface (Updated 3/25/01).
bulletDeep Viewer Tutorial by Gale Rhodes (Updated 3/25/01).
bulletDomainFinder 1.0new.GIF (Free only UNIX; Linux) is an interactive program for the determination and characterization of dynamical domains in proteins. Its key features are computational efficiency: even large proteins can be analyzed using a desktop computer in a few minutes ease of use: a state-of-the-art graphical user interface export of results for visualization and further analysis (VRML, PDB, and MMTK object format) (Updated 6/14/99).
bulletEGO (Unix and PC (with GNU-c compiler); free downloadable)is a program to perform molecular dynamics simulations on parallel as well as on sequential computers at Bayerish Acadamie of Science, Munich, Germany (Updated 5/22/99).
bulletFTDock, RPScore and MultiDock
bulletGAMESS Home Page (Unix, VMS, MVS, VM, Mac, or PC; free downloadable Software) for doing ab initio calculations at Ames Laboratory/Iowa State University (Updated 5/22/99).
bulletDescription: GAMESS can compute wavefunctions ranging from RHF, ROHF, UHF, GVB, and MCSCF, with CI and MP2 energy corrections available for some of these (Updated 5/22/99).
bulletGROMACS (Unix, and PC (in the future), free downloadable for non-commercial users) is a useful suite of molecular modeling utilities available at Chemistry department University of Groningen (Updated 5/22/99).
bulletGROMOS (GROningen MOlecular Simulation) new.GIF (3043 bytes)(free for academic usage; Unix?) is a general-purpose molecular dynamics computer simulation package for the study of biomolecular systems.  The site is maintained at ETH(Updated 7/17/99).
bulletMEPSIM distribution (Code obtainable through email; Website currently under construction) for Molecular Electrostatic Potential SIMilarity Analysis (Updated 5/22/99)
bulletDescription: New features of the program will include the possibility of performing GAMESS and GRID calculations within the package, taking profit of the MEPSIM modules (Updated 5/22/99).
bulletMOLGEN (MSDOS; free downloadable) automatic structure elucidation (FTP site)(Updated 5/22/99)
bulletDescription: This software allows the user to do various calculations (i.e. HOMO, LUMO, potential) on small molecules (Updated 5/22/99).
bulletMOLSCAT (UNIX; free downloadble) is a code for quantum mechanical (coupled channel) solution of the nonreactive molecular scattering problem (Updated 5/22/99).
bulletMolScript (UNIX; free for non-profit, but license required) Official Homepage by Avatar Software AB, who develops, markets and distributes software for structural biology, protein NMR and bioinformatics (Updated 5/22/99).
bulletDocumentation
bulletDescription: MolScript is a program for creating schematic or detailed molecular graphics images from molecular 3D coordinates, usually,
but not exclusively, protein structures (Updated 5/22/99).
bulletMolecular Structure Editornew.GIF with the complete source code in C and x86 assembler language and can rotate a molecule of 5000 atoms drawn with nice realistically looking balls and sticks on a lowly 80386/16MHz and can be configured to read output files generated by almost any popular quantum-chemical application (Updated 6/14/99).
bulletMMTK (UNIX (Requires Python); free downloadable) Molecular Modelling Toolkit (MMTK) is a program library for molecular modelling applications at Theoretical biophysics at the CBM (Updated 5/22/99).
bulletDescription: MMTK provides researchers, especially those working on the development of new simulation and modelling methods, with a code basis that can be easily extended and modified to deal with standard and non-standard problems in molecular modelling (Updated 5/22/99).
bulletMOE (UNIX and Windows, proprietary)  the Molecular Operating Environment is the next generation of chemical computing software. MOE is an integrated Applications Environment and Methodology Development Platform. MOE integrates visualization, simulation and application development in one package (Updated 5/13/01).
bulletNAMD Home Page (UNIX; free downloadable, but registration required ) is a parallel, object-oriented molecular dynamics code designed for high- performance simulation of large biomolecular systems at the Theoretical Biophysics Group of University of Illinois at Urbana. (Updated 5/22/99)
bullet SCWRL - Sidechain placement With a Rotamer Librarynew.GIF  ( Unix; free for academic users ) is a program for adding sidechains to a protein backbone based on the backbone-dependent rotamer library. The library provides lists of chi1-chi2-chi3-chi4 values and their relative probabilities for residues at given phi-psi values, and explores these conformations to minimize sidechain-backbone clashes and sidechain-sidechain clashes (Updated 9/23/99).
bulletSwiss PDB Viewer  new.GIF(free for PC and Macintosh) is an application that provides a user friendly interface allowing to analyze several proteins at the same time. The proteins can be superimposed in order to deduce structural alignments and compare their active sites or any other relevant parts. Amino acid mutations, H-bonds, angles and distances between atoms are easy to obtain thanks to the intuitive graphic and menu interface (Updated 3/25/01).
bulletSwiss PDB Viewer Tutorial by Gale Rhodes (Updated 3/25/01).
bulletTINKER Molecular Modeling Package, (PC; free downloadable) it is a program that accepts a variety of different parameter files from a variety of different molecular dynamics packages, including AMBER, and CHARMM (Note: Trouble connecting to server 5/22/99, Updated 5/22/99).
bulletMolda is a Graphics interface for Tinker.  Note: the Tinker server is sometimes down, so in the near future I will try to make copies available to this site. (Updated 5/22/99)
bulletViewmol (Unix; free downloadable) is a graphical front end for computational chemistry programs.  It is able to graphically aid in the generation of molecular structures for computations and to visualize their results.  The program has many features. (Updated 7/15/99)
bulletVMD
bulletNAMD (Unix and Free)is a parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD is distributed free of charge and includes source code. 
bulletWHAT IF (UNIX and PC; proprietary) is a versatile protein structure analysis program that can be used for mutant prediction, structure verification, molecular graphics, etc. at the EMBL Heidelberg Germany, BIOcomputing unit, 3D modeling, protein structure analysis. (Updated 5/22/99)
bulletWHAT IF (web interface) (platform independent; Free) provides nearly 2000 options in fields as diverse as
homology modeling, drug docking, electrostatics calculations, structure
validation and visualisation (Updated 6/9/99).
 

Friday, November 22, 2013

Saturday, October 12, 2013

https://www.youtube.com/watch?v=ZNfVnxmZQZE&feature=youtube_gdata_player

Saturday, June 08, 2013

Books and Articles

  1. 1000 Most Common Words in English - Numbers Vocabulary for ESL EFL TEFL TOEFL TESL English Learners.xls
  2. 1306.1527.pdf
  3. A Critique of Pure String Theory - Heterodox Opinions of Diverse Dimensions.pdf
  4. A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules.pdf
  5. A quantum mechanical polarizable force field for biomolecular interactions.pdf
  6. Adobe Photoshop CS for Photographers_Martin Evening 2004.pdf
  7. Alvaro Azevedo - Mecanica Dos Solos - PT.pdf
  8. Application of a Universal Force Field to Main Group Compounds. J.Am.Chem.SOC.1992,114,10046-10053.pdf
  9. Application of a Universal Force Field to Organic Molecules.pdf
  10. Comp Sim of Urea-Water Mixtures. A Test of Force Field Parameters for Use in Biomolecular Simulation.pdf
  11. Development and Testing of a General Amber Force Field.pdf
  12. Development of Polarizable Water Force Fields for Phase Equilibrium Calculations.pdf
  13. Dynamical fluctuating charge force fields. Application to liquid water. J.Chem.Phys.,Vol.101,No.7,1994.pdf
  14. Effects of the polarizability and water density constraint on the structure.pdf
  15. Electrohydrodynamics_of_Charged_Surfaces.pdf
  16. Elena Hurberger - What Counts-chap2.pdf
  17. Fizicheskie_osnovy_kriobiologii.pdf
  18. Force Field Influence on the Observation of -Helical Protein Structures in Molecular.pdf
  19. Force field parametrization by weak coupling.Re-engineering SPC water.pdf
  20. Force-field parametrization and molecular dynamics simulations of Congo.pdf
  21. Fundamental_light_source_and_lasers.pdf
  22. Fundamentals of Electric Circuits 4th ed - C. Alexander, M. Sadiku (McGraw-Hill, 2009) WW.pdf
  23. Games-Course Technology 3D Game Programming All In One Ebook-Lib.chm
  24. Haisch - Inertia as zero-point-field Lorentz force (1994).pdf
  25. Lawler_G.F._Introduction_to_stochastic_processes_(Chapman-Hall,_1995)(ISBN_0412995115)(K)(T)(188s)_MVspa_.pdf
  26. Lecture.Notes.on.Elementary.Topology.and.Geometry, I.M.Singer.And.J.A.Thorpe.pdf
  27. Lectures on metaphysics and logic (vol 4) - Hamilton.pdf
  28. Materials Science and Engineering Handbook. CHAPTER 4 Thermodynamic and Kinetic Data.pdf
  29. Materials Science and. CHAPTER 14 Selecting Electrical Properties.pdf
  30. Math.MIT Press.Encyclopedic Dictionary of Mathematics Complete.pdf
  31. Mathematics_for_Physics_I.pdf
  32. Mod.of.helix.rev.def.in.polyt.Force field development.pdf
  33. Modelirovanie_na_JeVM_atomnyh_konfiguraciy_defektov_v_metallah.pdf
  34. Molecular force field development for saccharides using the SPASIBA spectroscopic potential.pdf
  35. Nature of force acting on charged classical particle deviated from its geodesic path.pdf
  36. New English File - Pre-intermediate Workbook Key.pdf
  37. New Headway English Course - Beginner (Tests) [Julia Starr Keddle] [found via www.FileDonkey.com].pdf
  38. New Headway English Course - Upper-Intermediate [found via www.FileDonkey.com].pdf
  39. Novaya_Zhizn_Polnoy_Integriruemosti.pdf
  40. Novel Self-Assembled Chain of Water Molecules in a Metal-Organic Framework Structure.pdf
  41. Novosti_Fiziki_v_Seti_Internet_Tom183_N4.pdf
  42. Novosti_Fiziki_v_Seti_Internet_Tom183_N5.pdf
  43. Osnovnye_Etapy_Atomnogo_proekta.pdf
  44. Osnovnye_Uravneniya_Kvantovoj_Mehaniki.pdf
  45. Parametrization of Backbone-Electrostatic and Multibody Contributions to the UNRES Force Field.pdf
  46. Physics - Encyclopedia of Astronomy and Astrophysics.pdf
  47. Quantum Mechanics.pdf
  48. Quantum-Chemical and Force-Field Investigations of Ice Ih. Computation of Proton-Ordered Structures.pdf
  49. Relyativistskie_zerkala_v_plazme.pdf
  50. Relyativistskoe_Volnovoe_Uravnenie_Electrona.pdf
  51. Staticheskie_Svoystva_Dinamicheskogo_Khaosa.pdf
  52. Steen_Effects of Roads on the Structure of Freshwater Turtle.pdf
  53. Structure and Stability of Water Clusters (H2O)n, n) 8-20. An Ab Initio Investigation.pdf
  54. Structure and dynamics of water at the interface with phospholipid bilayers.pdf
  55. Strukturnye_modeli_vody.pdf
  56. Study of the hydronium ion in water. A combined quantum chemical and statistical mechanical treatment.pdf
  57. The Nature Of The Universe, Its Form, Substance, Energy, Force, Character And Structure.pdf
  58. The electronic structure of liquid water within density-functional theory.pdf
  59. The properties of ion-water clusters. II. Solvation structures of Na+, Cl-, and H+ clusters.pdf
  60. Thomas_Differencial_Equations-16_First_Order-17_Second_Order.pdf
  61. UFF, a Full Periodic Table Force Field for Molecular Mechanics and Molecular Dynamics Simulations.pdf
  62. Valone - Harnessing The Wheelwork Of Nature - Tesla's Science Of Energy (2002).pdf
  63. Water Structure from Scattering Experiments and Simulation.pdf
  64. Water_Retaining_Structures_Design.pdf
  65. Winston S Churchill - The Story Of The Malakand Field Force(1).pdf
  66. Winston S Churchill - The Story Of The Malakand Field Force.pdf
  67. Zhizn_v_Fizike.pdf
  68. data_1_2.mdb
  69. eBook.Wrox_Press-Expert_One-on-One_J2EE_Design_and_Development.ShareHeaven.chm
  70. inorganic chemistry course-lecture5.ppt
  71. lc_physics_teachers_guide.pdf
  72. metod_molekuljarnoy_dinamiki.pdf
  73. vapor interface revisited using the Amoeba force fieldions.pdf

Метод молекулярной динамики

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Успехи физических наук, 1918–2013

Вейвлет-анализ в нейродинамике


Вейвлет-анализ в нейродинамике

 а,  б,  б,  в,  г,  д
а Международный институт нелинейной динамики, физический факультет, Саратовский государственный университет, Саратов, Российская Федерация
б Саратовский государственный университет им. Н.Г. Чернышевского, факультет нелинейных процессов, Саратов, Российская Федерация
в Институт высшей нервной деятельности и нейрофизиологии РАН, Москва, Российская Федерация
г Universidad Complutense de Madrid
д Саратовский государственный университет им. Н.Г. Чернышевского, физический факультет, г. Саратов
Представлен обзор результатов по применению непрерывного и дискретного вейвлет-преобразований в задачах нейродинамики. Основное внимание уделяется новым возможностям, которые предоставляет вейвлет-анализ в расшифровке информации, содержащейся в сигналах нейронных систем и сетей. Рассматривается применение вейвлетов для анализа 1)микроскопической динамики (уровень отдельных клеток или внутриклеточных процессов), 2) обработки сенсорной информации, 3) динамики групповой активности в нейронных ансамблях, 4) макродинамики ритмической активности головного мозга (по данным многоканальных электроэнцефалограмм). Обсуждается возможность выделения и классификации различных осцилляторных паттернов электрической активности головного мозга, а также создания систем мониторинга активности головного мозга с использованием методов, основанных на непрерывном вейвлет-анализе.
Текст: pdf(1,6 Мб)
  
PACS: 05.45.Tp, 05.45.Xt, 07.05.Mh, 87.19.L-, 95.75.Wx (все)
DOI: 10.3367/UFNr.0182.201209a.0905
URL: http://ufn.ru/ru/articles/2012/9/a/
Цитата: Павлов А Н, Храмов А Е, Короновский А А, Ситникова Е Ю, Макаров В А, Овчинников А А "Вейвлет-анализ в нейродинамике" УФН 182 905–939 (2012)
BibTexBibNote ® (generic)BibNote ® (RIS)MedlineRefWorks
Поступила: 6 октября 2011, доработана: 18 марта 2012, 20 марта 2012
English citation: Pavlov A N, Hramov A E, Koronovskii A A, Sitnikova E Yu, Makarov V A, Ovchinnikov A A “Wavelet analysis in neurodynamicsPhys. Usp. 55 845–875 (2012); DOI: 10.3367/UFNe.0182.201209a.0905

Физические основы криобиологии

Физические основы криобиологии


Физико-технический институт им. А.Ф. Иоффе РАН, Санкт-Петербург
Описаны физические явления на молекулярном, клеточном уровнях, на уровне тканей и органов в биологических объектах при замораживании и оттаивании. Рассмотрены основы криохирургических операций и криоконсервации клеток и тканей. Дан обзор моделей, включая численные, используемых в криобиологии.
Текст: pdf (417 Кб)
  
PACS: 44.05.+e, 81.10.-h, 87.15.Aa, 87.54.Br (все)
DOI: 10.3367/UFNr.0178.200803b.0243
URL: http://ufn.ru/ru/articles/2008/3/b/
Цитата: Жмакин А И "Физические основы криобиологии" УФН 178 243–266 (2008)
BibTexBibNote ® (generic)BibNote ® (RIS)MedlineRefWorks
English citation: Zhmakin A I “Physical aspects of cryobiologyPhys. Usp. 51 231–252 (2008); DOI: 10.1070/PU2008v051n03ABEH006449

Моделирование на ЭВМ атомных конфигураций дефектов в металлах

Моделирование на ЭВМ атомных конфигураций дефектов в металлах

Изложены кратко основные методы моделирования на ЭВМ атомных конфигураций дефектов в металлах и их перестроек — метод молекулярной динамики, вариационный метод, метод волн статических смещений. Обсуждаются новые потенциалы межатомного взаимодействия, в частности учитывающие частично заполненные d-оболочки переходных металлов. Приводятся типичные результаты расчетов атомных конфигураций дефектов и их энергий образования и миграции: смешанных гантелей, комплексов вакансия — примесный атом, кластеров из вакансий и межузельных атомов, структуры ядер дислокаций в ОЦК- и ГПУ-металлах, включая переходные, и в упорядочивающихся сплавах, границ зерен специальной разориентации, дефектов в суперрешетках пор в облученных металлах, дефектов в структуре аморфных металлов. Обсуждаются перспективы метода. Табл. 9, илл. 29, библиогр. ссылок 158 (172 назв.).
Текст: pdf(3,3 Мб)
  
DOI: 10.3367/UFNr.0142.198402b.0219
URL: http://ufn.ru/ru/articles/1984/2/b/
Цитата: Кирсанов В В, Орлов А Н "Моделирование на ЭВМ атомных конфигураций дефектов в металлах" УФН 142 219–264 (1984)
BibTexBibNote ® (generic)BibNote ® (RIS)MedlineRefWorks

Метод молекулярной динамики в статистической физике

Метод молекулярной динамики в статистической физике

 а,
а Институт теоретической и прикладной электродинамики РАН, г. Москва
Введение. Движение частиц в жидкостях и плотных газах. Проверка моделей движения частиц методом молекулярной динамики. Временная автокорреляционная функция скорости. Автокорреляционная функция сил в жидкости и плотном газе. Распад корреляций плотности. Продольные и сдвиговые волны в жидкости. Термодинамические свойства и явления переноса в простых жидкостях и плотных газах. Фазовые переходы. Термодинамические свойства простых жидкостей. Коэффициенты переноса. Расчетные схемы и точность метода молекулярной динамики. Динамика легкой классической частицы в плотной среде неупорядоченных тяжелых рассеивателей. Постановка задачи. Плотность состояний и пространственная корреляционная функция электрон — атом. Временная автокорреляционная функция скорости и изоэнергетическая проводимость. Расчет проводимости. Заключение. Цитированная литература.

Friday, May 24, 2013

GENERAL PHYSICS II | PHY 220, 4 credits, 3-hrs. lecture, 2-hrs. lab, 2-hrs. recitation

GENERAL PHYSICS II | PHY 220, 4 credits, 3-hrs. lecture, 2-hrs. lab, 2-hrs. recitation

Hostos Community College, Natural Science Department, Calculus Base Physics II

Final Exam, 2013 Spring



  1. A spherical surface (radius R = 1m) is uniformly charged (electric charge Q = 1 C). What the surface-tension T does this electric charge produce?
  2. An isolated system of three contacted solid bodies ( masses: m1,m2,m3, specific heat capacities: c1, c2, c3) have equilibrium temperature Tf . If initial temperatures of two bodies are known (T1, T2), what was the initial temperature T3 of third body?
  3. Three separately located capacitors (capacities: C1, C2, C3) with the electric charges: Q1, Q2, Q3 initially are not connected by conductors. Then capacitors have been connected by conductors into the open parallel circuit. What is the change of the total potential electric energy between the initial and final configuration.
  4. A spherical object (r < R) charged with the uniform electric charge density: ρ = 3Q/(4πR3).
    a) Find the electric field
    E=E(r), 0 ≤ r ≤ ∞ ;
    b) Find the electric potential
    V=V(r), 0 ≤ r ≤ ∞ .
  5. A spherical object (r < R) charged with the electric charge density: ρ = ρ(r) = Q/(2rR2).
    a) Find the electric field
    E=E(r), 0 ≤ r ≤ ∞ ;
    b) Find the electric potential
    V=V(r), 0 ≤ r ≤ ∞ .
  6. Four identical electric charges are located in the vertexes of a regular tetrahedron (triangular pyramid). Total electric potential energy of these electric charges is 6J. What will be the total potential energy of the same configuration if only one electric charge will change the sign.
  7. If three parallel resistors have the relation of their resistances (R1/R2/R3) as (1:2:3). What is the relation of currents (I1:I2:I3) on these parallel resistors?
  8. If three series resistors have the relation of their resistances (R1/R2/R3) as (1:2:3). What is the relation of voltages (V1:V2:V3) on these series resistors?
  9. In how many time will change the apparent weight of 100 kg man on the surface of the Earth, if each kilogram of the Earth mass will be charged by electric positive elementary charge, and each kilogram of the man mass will be charge by negative elementary charge?
  10. If loudness of the first sound source greater than loudness of the second sound source on the 30 Db. What is the ratio of the sound intensities I1/I2 ?
  11. Draw the rays diagram and calculate the position of the image if the object's location is 9 cm in front of converging lens with focal length 3cm.
  12. A plane sinusoidal electromagnetic wave in some transparent media is described for the electric field by equation: E=E(x,t)=Aj sin(Bx-Ct), where t is time, x is x-coordinate, j is unite vector to y direction.
    a) What is the direction of wave propagation?
    b) What is the wave speed?
    c) What is the refraction index of the transparent media?
    d) What is the frequency?
    e) What is the wave length?
  13. Unpolarized light passes through 5 parallel ideal polarizing filters. The angles between polarizing axis of two consecutive filters are identical and equal to 30 degrees. What is the ratio of the initial intensity to the final intensity of the light?
  14. Straight, infinitely long conductor with the current I produces the magnetic field B on the distance R from the conductor. What are possible magnetic fields on the central axis of three parallel infinite conductors with the same currents if the distance between any two conductors equals to R.













Tuesday, April 16, 2013

Thursday, March 21, 2013

Verrazano

Found this on Google Goggles: http://www.google.com/goggles/a/moments/zsHQY3pi6ogq1ri_w9m44SA?ogi=01090745990842414041