Tuesday, December 30, 2003

Thursday, December 18, 2003

Tuesday, December 16, 2003

Wednesday, December 10, 2003

Tuesday, December 09, 2003

"Stable calculation of coordinates from distance information" by G.M. Crippen and T.F. Havel, Acta Cryst. A34:282-284 (1978).

"Effects of distance constraints on macromolecular conformation. II. Simulation of experimental results and theoretical predictions" by T.F. Havel, G.M. Crippen and I.D. Kuntz, Biopolymers 18:73-81 (1979).

"A distance geometry study of ring systems: Application to cyclooctane, 18-crown-6, cyclododecane and androstanedione" by P. Weiner, S. Profeta, G. Wipff, T.F. Havel, I.D. Kuntz, R. Langeridge and P. Kolmann, Tetrahedron 39:1113-1121 (1983).

"The theory and practice of distance geometry" by T.F. Havel, I.D. Kuntz and G.M. Crippen, Bull. Math. Biol. 45:665-720 (1983).

"The combinatorial distance geometry approach to the calculation of molecular conformation. I. A new approach to an old problem" by T.F. Havel, I.D. Kuntz and G.M. Crippen, J. Theor. Biol. 104:359-381 (1983).

"The combinatorial distance geometry approach to the calculation of molecular conformation. II. Sample problems and computational statistics" by T.F. Havel, I.D. Kuntz and G.M. Crippen, J. Theor. Biol. 104:383-400 (1983).

"Shortest-path problems and molecular conformation" by A. Dress and T.F. Havel, Disc. Appl. Math. 19:129-144 (1988).

Tim Havel
Make Your Swing App Go Native, Part 1

Monday, December 08, 2003

rpb011: "Algorithms for Minimization without Derivatives"

Friday, December 05, 2003

Slashdot | So You Think Physics is Funny?

Q: What's purple and commutes?
A: An Abelian grape

Q: Why was Heisenberg's wife unsatisfied?
A: When he had the time he didn't have the energy, and when he had the position, he didn't have the momentum.

The pilot of a plane on its way out of Poland dies unexpectedly in flight. A passenger is asked to fill in. He looks at the controls and shakes his head. "What's wrong?" someone asks. The reply: "I'm just a simple Pole in a complex plane".

A neutron walks into a bar and asks "how much for a beer?" The bartender replies "for you, no charge."

I have a quantum car. Every time I look at the speedometer I get lost...

So there was an argument over what type of engineer God was, to have created man. Some suggested Electrical Engineer, given the complex neural network, others suggested Mechanical Engineer, given the amazing mechanics of the body. It was finally realized that he was a Civil Engineer, as only a Civ. E. would put an waste management facility in a recreational area.

WMAP Observatory_Lagrange Points
references : Java Glossary
RIAA Radar: Home

What is RIAA Radar?
The RIAA Radar is a tool that music consumers can use to easily and instantly distinguish whether an album was released by a member of the Recording Industry Association of America (RIAA).

Thursday, December 04, 2003

Tuesday, December 02, 2003

The Bioinformatics Center at Rensselaer and Wadsworth. I-Sites Overview

PROTEAN is a program for doing Brownian dynamics of polypeptides in torsion space using implicit solvent.

Tuesday, November 18, 2003

The DIIS Method: "Some Comments on Accelerating Convergence of Iterative Sequences Using Direct Inversion of the Iterative Subspace (DIIS) "
MPQC Home: "The Massively Parallel Quantum Chemistry Program"
Alternate View Column AV-83: "Antigravity Sightings"

Monday, November 17, 2003

Sunday, November 09, 2003

On the Behavior of the Gradient Norm in the Steepest Descent Method (ResearchIndex)

"It is well known that the norm of the gradient may be unreliable as a stopping test in unconstrained optimization, and that it often exhibits oscillations in the course of the optimization."

Saturday, November 08, 2003

Friday, November 07, 2003

Page of Milan Kunz

About Eigenvalues of Quadratic Distance Matrices of Alkanes

M. Kunz: On topological and geometrical distance matrices, J. Math. Chem., 13 (1993) 145-151.
Adjacency matrix - Wikipedia

If A is the adjacency matrix of the directed or undirected graph G, then the matrix An (i.e. the matrix product of n copies of A) has an interesting interpretation: the entry in row i and column j gives the number of (directed or undirected) paths of length n from vertex i to vertex j.
> C++ > Optimization

Thursday, November 06, 2003

Wednesday, November 05, 2003

Critical Section - The Emperor's New Code: "It was interesting that in Don Box' introduction to Indigo at the PDC, he asked the roomful of developers 'how many people have successfully deployed DCOM?' Nobody raised their hands. 'How many people have successfully deployed .NET remoting?' Nobody raised their hands. 'How many people have successfully deployed CORBA?' Only a few hands. Out of 3,000 developers essentially none had successfully deployed an object-oriented remote communication method. It is good that Microsoft has abandoned OO and embraced SOA."

Tuesday, November 04, 2003

Saturday, November 01, 2003

Thursday, October 30, 2003

San Diego Was In No Shape for This Fight:

"For at least a generation, attempts in San Diego to raise taxes to boost fire protection have been largely defeated. In the past 25 years, 32 of 50 ballot measures aimed at raising money for fire protection in the county have failed.

'San Diegans are cheap,' said Steve Erie, professor of political science at the University of California, San Diego, and an expert in the funding of local government. 'We've come to rely on the kindness of outsiders in terms of mutual aid. It's the result of politicians who follow rather than lead.'"
Northern Hemisphere Enlarged View : POES Auroral Activity
OEChem or OELib?

Monday, October 27, 2003

Saturday, October 25, 2003

"Extreme Deprogramming"

"Refactoring has been abducted from its proper home in the algebraic texts and elevated to the status of an essential work method, which one must apply ruthlessly. If we consider that rework or restructuring are essentially synonyms for refactoring, we see that this piece of custom terminology is only dignifying the act of investing effort to correct ill-considered implementation decisions for no functional gain."

"Whether you choose to label XP a cult is not as important as whether you recognize that it displays cult-like attributes. I believe that the psychological and social phenomenon underlying these six characteristics account in no small part for the current popularity that XP enjoys. I also believe that they point to its future.
Cults tend to have a very limited life. The hype and fervor can only sustain the devotion of the members for so long, and eventually they will look to other sources for inspiration – those leaving a cult are frequently drawn into another within a short time.

I believe that XP will eventually lose its luster and fall into disrepute like so many other religious, commercial and technical cults of the past. Many of the current adherents will cast about for a new cause to follow, and no doubt the marketing departments of the technical book publishers and software vendors will be only too happy to provide them with a new subject upon which to focus their devotion. Meanwhile, software projects will continue to fail or succeed with the same frequency as always, as our industry continues its search for a panacea to the ills of software development."

"The very first line within the agile manifesto reads 'Individuals and interactions over processes and tools.' In fact, XP involves the process over the person by way of one-size fits all straightjacket that confines individuality and creativity. Say goodbye to your IDE with custom fonts suited to your own personal taste. Say goodbye to a small collection of your favorite books. Say goodbye to a picture of the family next to your favorite coffee mug. These are personal items and do not have a place in the XP lab. Its goal is the depersonalization of each developer into 'work units'. The actual stated goal of XP is to render each developer obsolete, by way of their being replaceable at any given time. There is to be no specialization, save specialization in XP itself."
The Pragmatic Programmers, LLC: "Pragmatic Starter Kit"

Friday, October 24, 2003

Take Back Your Time Day
Creo Tokens - Creo: "A Token is like a shortcut or alias that you can send via e-mail or instant message. With just one click you can create a token, and no matter how large the files you want to send are, the token representing them will be very small - just a few KB. Anyone you send a token to can then download the free Creo Token Redeemer software, and with one click redeem the token and download the files. It works for anything - a single file, an entire folder, a huge movie."
C# Language

Includes a link to the C# 2.0 specification which includes generics.

Thursday, October 23, 2003

"The Illusion of Conscious Will" by Daniel M. Wegner

In the end Wegner is unable to give up on the idea that we WILL our actions. He devotes a book to saying this is an illusion, but ultimately he does not want to give up on will as a causal force and that was a disappointment.
The Hacker's Diet

Stress is a primary cause of overeating and weight gain.
TypeLogic Home Page

Myers-Briggs typology

ISFJ 89 11 33 11
The Return of Jobs to India

"There is a profound historical irony here. Indian workers can outcompete British workers today because Britain smashed their ability to compete in the past. Having destroyed India's own industries, the East India Company and the colonial authorities obliged its people to speak our language, adopt our working practices and surrender their labour to multinational corporations. Workers in call centres in Germany and Holland are less vulnerable than ours, as Germany and Holland were less successful colonists, with the result that fewer people in the poor world now speak their languages."
Differences Among IEEE 754 Implementations

Wednesday, October 22, 2003

Tuesday, October 21, 2003

spiked-life | Column | Schooling Mum: "Education is stripped of its formal content, and presented as a means to an end - the end being, not a love of books or even basic literacy, but social inclusion."
flooble :: fun(?) stuff :: Genesis Project Notes
JCSC: "JCSC is a powerful tool to check [Java] source code against a highly definable coding standard and potential bad code."

Monday, October 20, 2003

Principles Vs Sociability: "Principles don't conflict with social behavior. Principles are about what you believe, social behavior is about how you interact with people. You can hold any principle to any degree and still be nice about it, unless one of your principles is to be mean."
Shirky: A Group Is Its Own Worst Enemy

Thursday, October 16, 2003

Death and Taxes? The Estate Tax Repeal and American Democracy [pdf]
Inversion Angle Potentials

DL_POLY_3 USER MANUAL - W. Smith, CCLRC, Daresbury Laboratory, Daresbury, Warrington WA4 4AD, England.

Wednesday, October 15, 2003

"Efficient characterization of stationary points on potential energy surfaces". Peter Deglmann and Filipp Furche, The Journal of Chemical Physics Vol 117(21) pp. 9535-9538. December 1, 2002
The TURBOMOLE Documentation Page
The Woolly-Thinkers Guide to Rhetoric

Tuesday, October 14, 2003

Thursday, October 09, 2003

Java Remote Method Invocation: "Java Remote Method Invocation (RMI)"
Crystal Research and Technology: "Journal for Experimental and Industrial Crystallography"
CNN.com - Brain pain the same for ego blow, physical punch - Oct. 9, 2003:
"To a part of the brain that registers pain, the distressful reaction from social rejection is just as great as from a poke in the eye, according to researchers who measured the neural reactions of people who thought they had become outcasts in a game."

Summary : Panksepp, NEUROSCIENCE: Feeling the Pain of Social Loss, Science 2003 302: 237-239
Universal Force Field: "Universal Force Field FAQ"
Description of MCM: "A Description of the Molecular Classical Mechanics (MCM) Software"

Tuesday, October 07, 2003

The Explicit Hydrogen-Bond Term
NAMD - Scalable Molecular Dynamics
CNN.com - Study: Being fat at 40 cuts years off life - Jan. 6, 2003:
"'If you're overweight, you basically live three years less ... and if you're obese, you live approximately six to seven years less,' says Dr. Robert Eckel with the American Heart Association."
How to read your cat's body language

Cat body language
Recent Earthquakes - Info for A minor earthquake
"A minor earthquake occurred at 10:35:51 AM (PDT) on Tuesday, October 7, 2003.
The magnitude 3.9 event occurred 6 km (4 miles) W of San Ysidro, CA.
The hypocentral depth is 16 km (10 miles). "
Google Web Search Features: "How to use the Google calculator"
the 2003 demotivators® collection
Web OC: "Changes to the Default Handling of ActiveX Controls by Internet Explorer "

Friday, October 03, 2003

Getting Started with Tcl - Tcl Developer Xchange
Comparison USA-Germany
Leaping, Then Looking: "You want to lower costs. You will be managing projects globally. But the move of programming and other top jobs abroad has implications for national security. And you just might be creating your next rival."

Wednesday, October 01, 2003

about Vim : vim online: "Vim is an advanced text editor that seeks to provide the power of the de-facto Unix editor 'Vi', with a more complete feature set."

Tuesday, September 30, 2003

Lean Software Development (pdf)
Handles: "A Handy Guide To Handling Handles"

Saturday, September 27, 2003


Zhongwen.com contains the complete text of Amazon's best selling, best reviewed Chinese-English dictionary : Chinese Characters: A Genealogy and Dictionary, which uses the new (zipu) system of character trees.

Learning Chinese Online

Friday, September 26, 2003

The potential power of 'Software Patents' to destroy Crystallographic Software; Crystallographic Software Development; and Crystallography's Future. by Lachlan M. D. Cranswick - part of Software Patents Involving Crystallography - CCP14 Homepage

Many Software Patents patent the trivial, but describe their claims in complicated "patent speak". This can also help mask the patenting of an "idea", as though it was really a novel, non-trivial "invention".

Wednesday, September 24, 2003

Macrophage and Bacterium 2,000,000X
Jörg's USEFUL and UGLY pages
LLL algorithm:

A lattice reduction algorithm, named after discoverers Lenstra, Lenstra, and Lovasz (1982), that produces a lattice basis of "short" vectors.

Lenstra, A. K.; Lenstra, H. W.; and Lovasz, L. "Factoring Polynomials with Rational Coefficients." Math. Ann. 261, 515-534, 1982.

Keith Matthews' LLL page
No Title: "Basis Reduction Algorithms and
Subset Sum Problems "
Kovar/Hall: "Electron Band Structure In Germanium, My Ass"

Tuesday, September 23, 2003

ACE : a GAP 4 package - Chapters
Advanced Coset Enumerator

Coset Enumeration
GAP - Groups, Algorithms and Programming.
3-D Crystals: "The Total Symmetry of Three-dimensional Crystals"

Sunday, September 21, 2003

Java Desktop System
Mystic Microsoft:� Spiritual Transformation in the Halls of High Technology by Kraig Brockschmidt
Soapbox: Humans should not have to grok XML: "Humans should not have to grok XML"
grieve with me, blue master chickenz: "bloody hell, you left it turned on all night!"
A garbage collector for C and C++

The Boehm-Demers-Weiser conservative garbage collector can be used as a garbage collecting replacement for C malloc or C++ new.

Friday, September 19, 2003

"Ebenfalls sind zu grosse Ordnung, wenn sie nicht betrieblich notwendig ist, uebertriebene Gruendlichkeit und allzu umfangreiches Berichtschreiben meist ein Zeichen, dass die MitarbeiterInnen keine sinnvollen und herausfordernden Aufgaben haben, es ihnen also langweilig ist."
Langeweile braucht Herausforderungen
Wired News: China Threatens India Eminence: "China Threatens India Eminence"
[Article published 2/23/2001]
There is a lot of wasted time and productivity in a typical construction project.
Rethinking Hybridization
Effective XML

Thursday, September 18, 2003

Mothering Magazine -- Boredom The Cauldron of Creativity:
"Over the years, I moved reluctantly through boredom's idle territory. I would be a different person today without the paths that it delivered. For boredom often pressed me to say 'yes' to strange tasks and exotic foods. It nudged me to read extraordinary books, to take walks and talk to strangers. Boredom has volunteered me, sent me to foreign countries, and pushed me out of dead-end jobs. Boredom led me to believe that the only way forward is through. "
"When we respond to boredom's invitation, something magical happens. Passions are born. Interests are developed. An inner fund of resources evolves-the same personal resources that guide and prompt us into a meaningful life. Without this fund, boredom can push our children into self-destruction: drugs, violence, and random pranks that eat up their young lives and spit them out. We are left to pick up the pieces and wonder what went wrong.

We are rightfully fearful of boredom and its negative consequences. Too much time and money, little purpose, and boredom are a lethal combination. In an attempt to save our children, we sign them up for sports and classes. We let them watch a crazy amount of television and spend days at the computer.

I want to allow my children to be bored while they are young and under my watchful eye. To measure it into their bones and muscles like a rare fuel to propel them forward. To preempt the time spent on television and organized activities and have them spend it instead on claiming their imaginations. For in the end, that is all we have. If a thing cannot be imagined first-a cake, a relationship, a cure for AIDS-it cannot be.

Life is bound by what we can envision. I cannot plant imagination into my children. I can, however, provide an environment where their creativity is not just another mess to clean up but welcome evidence of grappling successfully with boredom. It is possible for boredom to deliver us to our best selves, the ones that long for risk and illumination and unspeakable beauty. If we sit still long enough, we may hear the call behind boredom. With practice, we may have the imagination to rise up from the emptiness and answer."

GameDev.net - Do We Really Need Quaternions?

Quaternions were developed by William Rowan Hamilton around 1843 and immediately took their place in mathematical history as a solution in search of a problem.
Use Bizarre Metaphors: "If you can't find your toothbrush, look where the cat sleeps."
National Center for Education Statistics (NCES) Home Page, a part of the U.S. Department of Education
BBC NEWS | Education (7/30/2003) | California protects education budget: "California has almost six million pupils in its school system and over 500,000 students in its universities. "

Wednesday, September 17, 2003

Introduction to CML
Schlegel Group - Dept. of Chemistry, Wayne State University, Detroit, MI, USA
TheBrain Technologies Corporation
Review of Principles and Applications of Stereochemistry: "Book Review -
Principles and Applications of Stereochemistry"
SVG for Designers: Chapter 8 Excerpts: "Incorporating SVG in Web Sites"
gladwell dot com / The Social Life of Paper: "The mark of the contemporary office is not the file. It's the pile."

Tuesday, September 16, 2003

Is a Calorie Always a Calorie?
From highlights of "Education at a Glance," the annual report from the Organization for Economic Cooperation and Development:

The United States spends more in public and private money on all levels of education -- about $10,240 per student in 2000 -- than any other country.

Saturday, September 13, 2003

Friday, September 12, 2003

Psychobiology of Boredom

Boredom may be defined as the suspension of intentionality, fidgety indifference, frustration, and painful estrangement from a reality experienced as meaningless. Normal boredom emerges in specific environmental situations (reactive boredom) and quickly dissolves (acute boredom), while pathological boredom, arising unrelated to external circumstances (endogenous boredom), becomes a pervasive and long-lasting cognitive-affective state (chronic boredom) and causes mental suffering as well as functional and social impairment. To overcome this painful condition, behavioral attempts (eg, making journeys, compulsive buying, gambling, nicotinism, or bulimia) and/or pharmacologic attempts (ie, substance abuse and dependence) are frequently made.
Space-Filling Curve Sculpture and Pictures
CTRL+F4 to close MDI window,
CTRL+F6 to cycle through them.

Thursday, September 11, 2003

Post, then Publish.
Nothing is interesting , if you are not interested.
[Helen MacInnes]