Lecture 1 for BIOS 203 Mini-course at Stanford University taught by Heather J. Kulik. http://bios203.stanford.edu for more info or email bios203.course@gmail.com
Lecture 7 of BIOS 203 mini-course taught by Heather Kulik at Stanford University. Rare event techniques. http://bios203.stanford.edu or email bios203.course@gmail.com for more information.
In this talk I will discuss different approximations in DFT: pseduo-potentials, exchange correlation functions.
The presentation can be downloaded here:
http://www.attaccalite.com/wp-content/uploads/2022/03/dft_approximations.odp
Lecture 7 of BIOS 203 mini-course taught by Heather Kulik at Stanford University. Rare event techniques. http://bios203.stanford.edu or email bios203.course@gmail.com for more information.
In this talk I will discuss different approximations in DFT: pseduo-potentials, exchange correlation functions.
The presentation can be downloaded here:
http://www.attaccalite.com/wp-content/uploads/2022/03/dft_approximations.odp
In computational physics and Quantum chemistry, the Hartree–Fock (HF) method also known as self consistent method is a method of approximation for the determination of the wave function and the energy of a quantum many-body system or many electron system in a stationary state
(This presentation is in .pptx format, and will display well when embedded improperly, such as on the SlideShare site. Please download at your discretion, and be sure to cite your source)
Review of the Hartree-Fock algorithm for the Self-Consistent Field solution of the electronic Schroedinger equation. This talk also serves to highlight some basic points in Quantum Mechanics and Computational Chemistry.
March 21st, 2012
Lecture 5: Introduction to Quantum Chemical Simulation graduate course taught at MIT in Fall 2014 by Heather Kulik. This course covers: wavefunction theory, density functional theory, force fields and molecular dynamics and sampling.
In computational physics and Quantum chemistry, the Hartree–Fock (HF) method also known as self consistent method is a method of approximation for the determination of the wave function and the energy of a quantum many-body system or many electron system in a stationary state
(This presentation is in .pptx format, and will display well when embedded improperly, such as on the SlideShare site. Please download at your discretion, and be sure to cite your source)
Review of the Hartree-Fock algorithm for the Self-Consistent Field solution of the electronic Schroedinger equation. This talk also serves to highlight some basic points in Quantum Mechanics and Computational Chemistry.
March 21st, 2012
Lecture 5: Introduction to Quantum Chemical Simulation graduate course taught at MIT in Fall 2014 by Heather Kulik. This course covers: wavefunction theory, density functional theory, force fields and molecular dynamics and sampling.
Challenges and Advances in Large-scale DFT Calculations on GPUs using TeraChemCan Ozdoruk
Recent advances in reformulating electronic structure algorithms for stream processors such as graphical processing units have made DFT calculations on systems comprising up to O(10 to the 3) atoms feasible. Simulations on such systems that previously required half a week on traditional processors can now be completed in only half an hour. Listen to Professor Heather Kulik, Massachusetts Institute of Technology, as she discusses how she leverages these GPU-accelerated quantum chemistry methods in the code TeraChem to investigate large-scale quantum mechanical features in applications ranging from protein structure to mechanochemical depolymerization. In each case, large-scale and rapid evaluation of electronic structure properties is critical for unearthing previously poorly understood properties and mechanistic features of these systems. Professor Kulik also discusses outstanding challenges in the use of Gaussian localized-basis-set codes on GPUs pertaining to limitations in basis set size and how she circumvents such challenges to computational efficiency with systematic, physics-based error corrections to basis set incompleteness
a detailed description of the structure of atom including all the discoveries and inclusion of those rules in periodic classification from Dr. Raghav Samantaray phd in applied chemistry (KIIT school of Biotechnology)
June 3, 2024 Anti-Semitism Letter Sent to MIT President Kornbluth and MIT Cor...Levi Shapiro
Letter from the Congress of the United States regarding Anti-Semitism sent June 3rd to MIT President Sally Kornbluth, MIT Corp Chair, Mark Gorenberg
Dear Dr. Kornbluth and Mr. Gorenberg,
The US House of Representatives is deeply concerned by ongoing and pervasive acts of antisemitic
harassment and intimidation at the Massachusetts Institute of Technology (MIT). Failing to act decisively to ensure a safe learning environment for all students would be a grave dereliction of your responsibilities as President of MIT and Chair of the MIT Corporation.
This Congress will not stand idly by and allow an environment hostile to Jewish students to persist. The House believes that your institution is in violation of Title VI of the Civil Rights Act, and the inability or
unwillingness to rectify this violation through action requires accountability.
Postsecondary education is a unique opportunity for students to learn and have their ideas and beliefs challenged. However, universities receiving hundreds of millions of federal funds annually have denied
students that opportunity and have been hijacked to become venues for the promotion of terrorism, antisemitic harassment and intimidation, unlawful encampments, and in some cases, assaults and riots.
The House of Representatives will not countenance the use of federal funds to indoctrinate students into hateful, antisemitic, anti-American supporters of terrorism. Investigations into campus antisemitism by the Committee on Education and the Workforce and the Committee on Ways and Means have been expanded into a Congress-wide probe across all relevant jurisdictions to address this national crisis. The undersigned Committees will conduct oversight into the use of federal funds at MIT and its learning environment under authorities granted to each Committee.
• The Committee on Education and the Workforce has been investigating your institution since December 7, 2023. The Committee has broad jurisdiction over postsecondary education, including its compliance with Title VI of the Civil Rights Act, campus safety concerns over disruptions to the learning environment, and the awarding of federal student aid under the Higher Education Act.
• The Committee on Oversight and Accountability is investigating the sources of funding and other support flowing to groups espousing pro-Hamas propaganda and engaged in antisemitic harassment and intimidation of students. The Committee on Oversight and Accountability is the principal oversight committee of the US House of Representatives and has broad authority to investigate “any matter” at “any time” under House Rule X.
• The Committee on Ways and Means has been investigating several universities since November 15, 2023, when the Committee held a hearing entitled From Ivory Towers to Dark Corners: Investigating the Nexus Between Antisemitism, Tax-Exempt Universities, and Terror Financing. The Committee followed the hearing with letters to those institutions on January 10, 202
Biological screening of herbal drugs: Introduction and Need for
Phyto-Pharmacological Screening, New Strategies for evaluating
Natural Products, In vitro evaluation techniques for Antioxidants, Antimicrobial and Anticancer drugs. In vivo evaluation techniques
for Anti-inflammatory, Antiulcer, Anticancer, Wound healing, Antidiabetic, Hepatoprotective, Cardio protective, Diuretics and
Antifertility, Toxicity studies as per OECD guidelines
Operation “Blue Star” is the only event in the history of Independent India where the state went into war with its own people. Even after about 40 years it is not clear if it was culmination of states anger over people of the region, a political game of power or start of dictatorial chapter in the democratic setup.
The people of Punjab felt alienated from main stream due to denial of their just demands during a long democratic struggle since independence. As it happen all over the word, it led to militant struggle with great loss of lives of military, police and civilian personnel. Killing of Indira Gandhi and massacre of innocent Sikhs in Delhi and other India cities was also associated with this movement.
How to Make a Field invisible in Odoo 17Celine George
It is possible to hide or invisible some fields in odoo. Commonly using “invisible” attribute in the field definition to invisible the fields. This slide will show how to make a field invisible in odoo 17.
2024.06.01 Introducing a competency framework for languag learning materials ...Sandy Millin
http://sandymillin.wordpress.com/iateflwebinar2024
Published classroom materials form the basis of syllabuses, drive teacher professional development, and have a potentially huge influence on learners, teachers and education systems. All teachers also create their own materials, whether a few sentences on a blackboard, a highly-structured fully-realised online course, or anything in between. Despite this, the knowledge and skills needed to create effective language learning materials are rarely part of teacher training, and are mostly learnt by trial and error.
Knowledge and skills frameworks, generally called competency frameworks, for ELT teachers, trainers and managers have existed for a few years now. However, until I created one for my MA dissertation, there wasn’t one drawing together what we need to know and do to be able to effectively produce language learning materials.
This webinar will introduce you to my framework, highlighting the key competencies I identified from my research. It will also show how anybody involved in language teaching (any language, not just English!), teacher training, managing schools or developing language learning materials can benefit from using the framework.
Model Attribute Check Company Auto PropertyCeline George
In Odoo, the multi-company feature allows you to manage multiple companies within a single Odoo database instance. Each company can have its own configurations while still sharing common resources such as products, customers, and suppliers.
Macroeconomics- Movie Location
This will be used as part of your Personal Professional Portfolio once graded.
Objective:
Prepare a presentation or a paper using research, basic comparative analysis, data organization and application of economic information. You will make an informed assessment of an economic climate outside of the United States to accomplish an entertainment industry objective.
2. Welcome to BIOS 203!
• Objective: to introduce students to the theory and application of a
variety of computational simulations methods.!
• Instructors: Dr. Heather Kulik, Dr. Lee-Ping Wang, Professor Todd
Martinez, Professor Tom Markland, Professor Vijay Pande.!
• TAs: Martinez group members: Sofia Ismailov, Liguo Kong, Sara
Kokkila, Aaron Sisto, Fang Liu, Brendan Mar.!
• When: Monday, Wednesday, Friday 9am-11:50am (lecture
9am-10am, lab work 10am-11:50am).!
• Grade (letter students): two lab assignments + one presentation
(credit students): presentation is optional.!
3. Mini-course schedule!
Mon, Feb 25! Course introduction,
empirical potentials and
minimizations
(Dr. Heather Kulik)!
Wed, Feb 27! Electronic structure basics Fri, Mar 8! Guest lecture: Markov
(Dr. Heather Kulik)! state models (Prof. Vijay
Pande)!
Fri, Mar 1! Classical molecular Mon, Mar 11! Transition state theory and
dynamics (Dr. Lee-Ping rare event techniques
Wang)! (Dr. Heather Kulik)!
!
Mon, Mar 4! Ab initio molecular Wed, Mar 13! Guest lecture: Free energy
dynamics (Dr. Lee-Ping methods (Prof. Tom
Wang) ! Markland)!
Wed, Mar 6! Guest lecture: Excited Fri, Mar 15! Methods for bioinorganic
states, mixed methods chemistry, presentations
(Prof. Todd Martinez)! (Dr. Heather Kulik)!
Lab 1 due! Lab 2 due!
!
4. Optional background texts!
• F. Jensen “Introduction to Computational Chemistry” Wiley !
• W. Koch and M. C. Holthausen “A Chemistʼs Guide to Density Functional
Theory” Wiley-VCH!
• A. Szabo and N. S. Ostlund, “Modern Quantum Chemistry: Introduction to
Advanced Electronic Structure Theory” Dover!
!
• C. J. Cramer “Essentials of Computational Chemistry: Theories and Models”
Wiley!
• M. P. Allen and Tildesley “Computer simulations of Liquids” Oxford Science
Publishers!
• T. Schlick “Molecular Modeling and Simulation” Springer!
• D. A. McQuarrie and J. D. Simon “Physical Chemistry: A molecular
approach” University Science Books!
• D. Frenkel and B. Smit “Understanding Molecular Simulations: From
Algorithms to Applications” Academic Press!
!
Specific literature will be provided along with each lecture.!
5. Why simulations?!
Protein folding: how proteins fold and
misfold (Prof. Vijay Pande)!
Voelz, Bowman, Beauchamp, Pande. JACS (2010).!
6. Why simulations?!
Drug design: 2nd generation HIV protease inhibitor Kaletra!
See Cobb “Biomedical Computational Review” 2007 and references therein.!
7. Why simulations?!
Photochemistry for RNA bases: mechanisms for
alternative proton transfer between RNA bases.!
Golan et al. Nature Chem. (2012).!
8. Simulations beyond
biochemistry!
Materials Genome Project: Identifying elements that
substitute for each other, chemical trends…!
Hautier, G… Ceder, G. Chemistry of Materials (2010).!
9. Choosing a computational
model!
Empirical models – functional form with parameters
from experimental or other calculated data:!
!Pair potentials!
!Many body potentials!
More transferable!
More efficient!
! Best tool for the
Semi-empirical models – model Hamiltonians:! job? Depends on
!Tight binding! the job!!
!MNDO, AM1…!
!
Quantum mechanical models – approximations to the
Schrödinger equation:!
!Hartree-Fock!
!Density functional theory!
!Post-Hartree-Fock (Configuration interaction, MP2)!
10. Exercise: Choose a
computational journal article.!
• Letter grade students: select a journal
article that uses computation (at least 50% of
the article) that interests you.!
• Throughout the course, or consulting with the
lecturers, build up an understanding of the
material.!
• Last class: present and explain the methods
used in the article and the major findings.!
• Need inspiration? See us for a list of
suggested journal articles.!
11. Empirical model potentials!
1 N ! !
E = E 0 + # V ( Ri ! R j )
2 i, j"i
V(ΔR)!
• Species are repulsive for
small distances!
• Attractive for longer distances!
• Only need to calculate ΔR!
potentials for atoms within a
certain distance.!
15. Limitations of pair potentials!
Counts only bonds, not organization:!
!
=!
Nbonds = 3! Nbonds = 3!
16. Limitations of pair potentials!
Counts only bond length, no orientation or
angular effects (e.g. ethylene):!
Pair potentials:!
C-H, C-C bonds.!
!
θ
θ
No treatment: !
H-C-H angle, !
H-C-C-H dihedral.!
17. Limitations of pair potentials!
Preference for high number/high density of
bonds formed to lower total energy:!
!
!
!
Bond energy for blue atom on left is four times the right.!
In real systems: more bonds means lower energy/bond.!
18. Adding angular terms!
H2O Bending! Harmonic
works well!
!
Note:
derivative
should be set
to zero at 180o!
adapted from
Jensen!
19. Adding torsional terms!
Ethane eclipsed! Ethane staggered! Torsional potential is
steric, non-bonded
electrostatics.!
!
!
!
!
!
!
!
Periodicity needs
Energy
to be enforced,
e.g. ethane.!
0 60 120 180 240 300 360
Dihedral (degrees)
20. AMBER!
Assisted Model Building with Energy Refinement:
AMBER is a force field and a software package.
http://www.ambermd.org!
1) AMBER Force field: ffXX (year) peptides and nucleic
acids, some ions (Mg2+).!
2) GAFF (Generalized Amber Force Field): generalized
scheme for force field for any organic molecule based
upon topology.!
3) Parameter sets available on the web:
http://www.pharmacy.manchester.ac.uk/bryce/amber/!
21. The AMBER force field!
Vn
E= " kb (l ! l0 )2 + " ka (! ! ! 0 )2 + " 2 [1+ cos(n" ! "0 )]+
bonds angles torsions
!(1)! ! ! !(2)! ! ! ! ! !(3)!
1, 2, 3: Harmonic oscillator-like bonding, angular, torsional terms!
(! $12 ! r $ + N'1 N q q
6
N'1 N (
N'1 N
r0ij Cij Dij +
. . !i, j *# r & ' 2 # r & - + . . 4"! r + . . * r12 ' r10 -
*# ij &
0ij
# &-
i j
j=1 i= j+1 )" % " ij % , j=1 i= j+1 0 ij j=1 i= j+1* ij
) ij -,
! ! !(4)! ! ! ! !(5)! ! ! ! !(6)!
van der Waals ! !electrostatic ! !hydrogen bonding!
22. Things that are missing…!
More advanced force fields:!
– Cross terms: e.g. bend affects stretch
in a water molecule. !
bend!
– Polarizability from point charges or
multipoles: e.g. AMOEBA.!
– Bond breaking and formation: e.g.
ReaxFF.!
!
Not all advanced methods are
feasible for very large simulations. !
23. Generalized Amber FF!
Same functional form as AMBER but more general
(http://ambermd.org/antechamber/gaff.html):!
!
24. GAFF parameters!
• Bond constants, force constants, torsional
dependence: based on assigned bonding
topology (you or a code decides).!
• Across large test set: MP2/6-31g*,
MP4/6-31g* and Cambridge Structural
Database training set.!
• Charges for electrostatics from semi-
empirical methods or HF/6-31g*. Can
generate custom charges for each molecule.!
25. Optimizing on a PES!
N atoms, 3N-6 degree
potential energy
hypersurface. Simplify!!
!
For classical MD: biggest
bottleneck is counting all
the bonds, need neighbor
lists to limit cost of
summation.!
Minimizations/optimizations: finding our way to local or
global minima!
from H. B. Schlegel, Wayne State U.!
26. Features of a PES!
from H. B. Schlegel, Wayne State U.!
27. Energy minimizations!
Minimize:! Force = !"(Energy)
Gradient on our PES in # "f "f &
terms of all coordinates !f = % ,!, (
(internal, cartesian):!
$ "x1 "xn '
Any stationary point
For !f != ! 0
! ! !:! (a) local minimum,
(b) global minimum,
What we usually
want!!
(c) saddle point.!
!
28. Steepest descent!
Optimization direction:! g = !"E
!i g i
Update coordinates:! ri+1 = ri +
! gi
Reduce λ near minimum.!
Pros: Fast when far from minimum,
local minimization guaranteed.!
!
Cons: slow descent for certain
PESs, can oscillate near minimum.!
From E. Eliav,
Tel Aviv U!
29. Conjugate gradient!
Initial direction:! h 0 = g 0 = !"E
Update coordinates:! ri+1 = ri + ! hi
Next steps:! hi+1 = g i+1 + ! i+1hi
!
where:! (g ! g )g
! i+1 = i+1 2i i+1
! gi
!
Pro: Using history, faster
convergence near minimum.!
From E. Eliav,
Tel Aviv U!
30. The Hessian/Force matrix!
(3N-6)
" %
!2 f !2 f !2 f '
(3N-6)x(3N-6) matrix $ !
with elements:! $ !x12 !x1!x2 !x1!xn '
$ '
(3N-6)
$ !2 f !2 f 2
! f '
2
! f 2
!
H ij ( f ) = H ( f ) = $ !x2!x1 !x2 !x2!xn '
!xi!x j $ '
$ " " # " '
$ !2 f !2 f !2 f '
$ ! 2 '
$ !xn!x1
# !xn!x2 !xn ' &
Approximate PES around stationary point by harmonic potentials.!
31. The Hessian/Force matrix!
Diagonalize Hessian Eigenvalues:! Eigenvectors:!
(eigenvalue problem)! 2 normal
n ! k = m" k coordinates!
!l (k )
k j = !H l
ij i
(k )
Harmonic
i=1 frequencies!
minimum! maximum! saddle point!
εk>0! εk<0! εk>0, except one εj<0!
From E. Eliav, ωk
all real! ωk
all imaginary! one imaginary ωj
on RC!
Tel Aviv U!
32. Minimizations… in practice!
• Explicit Hessian methods accurate but
too expensive for large molecules (9N2,
27N3). Approximations, updating.
!
• In AMBER: SD,CG, BFGS, following
low freq modes for struct. change.!
• May use only CG (gradient history ~
implicit treatment of Hessian)
!
• Combinatorial explosion: large
molecules (eg.rotatable bonds), many
possible conformers. Need better ways
to seek out global minimum: genetic
algorithms, Monte Carlo, etc.!
33. Follow-up reading!
• Force fields for biological systems:!
– J. W. Ponder and D. A. Case, “Force fields for protein simulations” Adv. Prot. Chem.
(2003).!
– A. D. Mackerell “Empirical force fields for biological macromolecules: Overview and
issues” J. Comput. Chem. (2004).!
• Non-biological force fields:!
– H. Balamane, T. Halicioglu, W. A. Tiller “Comparative study of silicon empirical
interatomic potentials” Phys. Rev. B. (1992).!
– M. Finnis, Interatomic Forces in Condensed Matter, Oxford University Press (2003).!
– M. J. Buehler, A. C. T. van Duin, W. A. Goddard, III “Multiparadigm modeling of
dynamical crack propagation in silicon using a reactive force field” Phys. Rev. Lett.
(2006).!
• Optimization for biological systems:!
– P. M. Pardalos, D. Shalloway, and G. Xue “Optimization methods for computing global
minima of nonconvex potential energy functions” J. Global Opt. (1994).!
– I. Kolossvary and W. C. Guida “Low mode search. An efficient, automated
computational method for conformational analysis: application to cyclic and acyclic
alkanes and cyclic peptides.” JACS (1996).!
– B. Das, H. Meirovitch, and I. M. Navon “Performance of hybrid methods for large-scale
unconstrained optimization as applied to models of proteins” J. Comput. Chem.
(2003).!
– K. Zhu, M. R. Shirts, R. A. Friesner, and M. P. Jacobson “Multiscale optimization of a
truncated Newton minimization algorithm and application to proteins and protein-ligand
complexes.” JCTC (2007).!
Editor's Notes
Only an energy and length scale. Simplistic description that works well for weakly interacting systems like noble gases. Commonly employed in molecular simulations for some materials.
More parameters, good description of covalent bonds. We can fit these potentials to experimental properties, results from accurate simulations, phonons, etc.
Hydrogen bonding adds 0.5 kcal/mol to hbond to supplement. 12-10 suggested by pauling. Values are derived from high order MP2(?) quantum chemistry fittings. Though it is called the force field, the force is really the derivative.