You could spend your life on the first six pages of “Stick Control” and still not cover all the possibilities. Dynamics, accents, foot-hand, foot-foot, fast/slow, hands on top of foot patterns, feet on top of hand patterns, regroupings and accenting in 5-7-4 (regrouping of the 16 strokes per pattern), 7-5-4 (re-regrouping of the 16 strokes), yadda yadda. If you see the first six pages of Stick Control as just exercises, you miss the fantastic complexity YOU can introduce to constantly humble yourself while hovering over a practice pad.

The original post related to the PDFs below (link) provided two downloads. The first was all 65,536 R/L combinations for 16th note groupings (so full measures of 16th notes in 4/4 time). The second contained all 4,096 8th note triplet groupings (so full measures of 8th notes in 12/8 time, or 4/4 “jazz” triplets).

This first set is academically complete, but any sticking combination with more than 4 R’s or L’s in a row is just endurance overkill (and even 3 becomes a problem until you figure out your fingers or controlled rebounds). In the interest of having something a bit easier on the warm-up and coordination routine, six new PDFs are below that divide up the 16- and 12-note grouping PDFs into 16- and 12-note sets that contain no more than 2, 3, or 4 R’s or L’s in succession (including the repeat of the pattern as you hammer through X many times). In sticking with the Terry Bozzio theme of the ostinato description of the first post, one could call these “The Easy Teenage New York Versions” of the original series.

Some Practice Ideas

The usage styles are the same as before. I have discovered a few things in working through the 2 R/L triplet combination page that I’ll point out.

1. Work through the whole list once without a click to get comfortable with the patterns. Going in cold will only frustrate when you reach a pattern your hands just aren’t interested in playing correctly yet.

2. The best way to build independence is to overwork your brain. If you can do “the pattern” with your feet playing a pattern, great. Your voice makes for a great 5th limb, more so when you speak the time out loud (in-head counting doesn’t quite cut it).

3. Put your hands on different instruments (maybe obvious). R on bell, L on snare, etc.

4. Escher-ize the patterns (see the sticking pattern as two independent patterns, then try to merge them). There were more than a few patterns where my hands did not work for the first passes, specifically a few patterns where the RR or LL occurs at the end of one beat of three and the beginning of the next beat of three (RRL LRR, for instance)).

My solution was to stop trying to play the sticking pattern and instead focus on playing “one hand” of the pattern, then filling in the missing beats with the other hand. For instance…

RRL LRR LRL RRL

Gets reduced to only the right hand, so only play the pattern as…

RR_ _RR _R_ RR_

When that’s comfortable, fill in the empty spaces with the left hand, perhaps playing the L at half-volume (say “l”) so the R pattern still stands out…

RRl lRR lRl RRl

Two things may happen. The first is that trying to stop thinking in terms of clave and instead in terms of sticking combination will make you butcher the pattern again. That just means you need to practice the pattern longer. The second is that you’ll play this thing with your right hand, think to yourself “that’s kinda funky if I play that on the bell,” and you’ll discover a groove that is magically easier to play than you thought based on your previous mangling of the pattern.

The Files

For notes on their generation, see www.somewhereville.com/?p=1399.

2011december17_stone_boulder_16th_grouping_series_RR_LL.pdf

2011december17_stone_boulder_16th_grouping_series_RRR_LLL.pdf

2011december17_stone_boulder_16th_grouping_series_RRRR_LLLL.pdf

2011december17_stone_boulder_jazz_grouping_series_RR_LL.pdf

2011december17_stone_boulder_jazz_grouping_series_RRR_LLL.pdf

2011december17_stone_boulder_jazz_grouping_series_RRRR_LLLL.pdf

Ideas of pattern use abound. If something hits you as particularly profound, please send me a note (damian@somewhereville.com) and I’ll gladly added it to the list.

Given the importance of the use of these scores both in FASTQ and MAQ (for MAQ (for me), specifically using alignment quality scores from Illumina sequencing runs to monitor run and sample quality), I was a bit surprised to not find some complete work-up of the meanings, the scores, the glyphs coordinated to the scores, and the encoding interpretations of these scores in one location. The two (three) tables shown here hopefully provide a meaningful summary.

I should qualify that much of the background for this page was taken from four key places. First is the wikipedia entry for FASTQ. Second is the wikipedia entry for Phred quality score. Third is the Rosetta Stone of Phred Score interpretation in the form of the open access article: P. J. A. Cock, C. J. Fields, N. Goto, M. L. Heuer and P. M. Rice, “The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants.” Nucleic Acids Research, 2010, Vol. 38, No. 6, 1767–1771 doi:10.1093/nar/gkp1137. Fourth is seqanswers.com in various forms.

(Sanger) Phred Quality Scores

I refer you to the two wikipedia articles on FASTQ and Phred Quality Scores for historical content (and for a brief discussion of the processing of chromatogram data for the production of quality scores). Table 1 shows the Q[Phred] (Phred Q) from P[Phred] values (Probability (P) Of Wrong Base), then adds the ASCII glyph codes (Sanger “Q + 33″ Shift) and characters (Sanger “Q + 33″ ASCII GLYPH) for the original Phred scores (Phred scores 0-to-93 use ASCII characters 33-to-126 in the Sanger method – this is performed to keep the single-character associated letters readable) and the Illumina 1.3+ codes (Illumina 1.3+ “Q + 64″ Shift, using ASCII glyphs 64-to-126 to score from 0-to-62 on the “P” scale) and corresponding ASCII glyphs (Illumina 1.3+ “Q + 64″ ASCII GLYPH). This is all likely completely self-explanatory (or hopefully will be by the bottom of the post). For review, the relationship between Phred quality score Q[Sanger] and the base-calling error probability P is

Q[Sanger]= −10 * log₁₀P

or, re-written for the logarithmically challenged…

P = 10^[-Q/10]

An assumption going in when I was producing plots from the Q[Sanger] and Q[Solexa] data was that the “P” was the same value and the Solexa system simply opted to use the Odds (P/(1-P)) as their metric. A proper two-second consideration of the shape of the form of P and P/(1-P) would have lead to the immediate conclusion that something was afoot. The table columns on the left of the black bar in Table 2 (2A) are the Q[Solexa] values based on the use of the Q[Sanger] probabilities. This is here simply to show that they are, in fact, not the same and if you’ve spent any time wondering why you can’t adequately… manipulate Excel’s rounding tools to reproduce the Q[Solexa] integer values, this is why.

The probabilities obtained for Q[Solexa] were, in fact, worked backwards from the integer values of Q[Solexa] (having found no table online that gives a number-by-number summary of the probability or odds). For background, the Q[Solexa] values are obtained from:

Q[Solexa] = −10 * log₁₀[(P/1-P)]

With all three data sets, I reproduce a plot familiar to the FASTQ community below, showing the asymptotic behavior of the Q[Solexa] and Q[Sanger] values at high Q (which represent the lowest read errors. They approach one another because the numbers are simply too damn small on the plot). Also obvious from the plot is that the plots show poor agreement with each other in the range where the error probability is highest (so the entire analysis goes to pot as the data quality goes to pot [ed. Note for the international reader: “pot” refers to the device found in the water-closet). The grey line is a good plot of the wrong data (that in Table 2A).

The presentation of this data is likely complete overkill, but I have found it useful in discussion. Hopefully your having tables in front of someone during an explanation will help clarify that explanation.

Published in the Journal Of Computational And Theoretical Nanoscience. This paper has been as delayed in posting as the accepted article was long in printing, which was less time than the wait for the completion of the manuscript, which itself was massive compared to the time of the experiments themselves, which was fractional compared to how long it would have been without the NanoHive@Home crew that donated so much compute time to the project so long ago. First off…

Acknowledgements

This work would not have been possible without the enormous contribution of the NanoHive@Home participants, composed of over 6,000 worldwide volunteers and their computers.

For those that were part of the NHAH community and want to see what the final work looks like, please drop me a line [nhah@somewhereville.com] so we can properly settle up.

The Paper Itself

Analysis Of Diamondoid Mechanosynthesis Tooltip Pathologies Generated Via A Distributed Computing Approach

Damian G. Allis,^a* Brian Helfrich,^b Robert A. Freitas Jr.^c, and Ralph C. Merkle^c

a. Department of Chemistry, Syracuse University, Syracuse, NY 13244, USA
b. Helcorp, Maplewood, NJ, 07040, USA
c. Institute for Molecular Manufacturing, Palo Alto, CA 94301, USA

The results of a combined molecular dynamics/quantum chemistry pathology study of previously reported organic (diamondoid) tooltips for diamondoid mechanosynthesis (DMS) are presented. This study, employing the NanoHive@Home (NH@H) distributed computing project, produced 80,000 tooltip geometries used in 200,000 calculations optimized at either the RHF/3-21G or RHF/STO-3G levels of theory based on geometries obtained from high-energy molecular dynamics simulations to produce highly deformed starting geometries. These 200,000 calculations have been catalogued, grouped according to energies and geometries, and analyzed to consider potentially accessible defect structures (pathologies) for tooltip geometries either binding a carbon dimer (C2) feedstock or not containing the transported dimer feedstock. The transport and deposition of feedstock and the stability of the tooltip between dimer “loading” cycles are important geometries that must be considered as part of a tooltip stability analysis. The NH@H framework is found to be a useful method both for the study of highly deforming covalent geometries and, using lower-temperature MD simulations, for generating and optimizing molecular conformations (demonstrated using biotin, n-heptane, and n-octane in this study). The results of the pathology survey are discussed and general considerations for the exploration of DMS tooltip usability are explored.

DOI:dx.doi.org/10.1166/jctn.2011.1792

A Few Visuals From The Article

The purpose of the study was to explore the conformation space of potential tooltips for use in mechanosynthetic operations. Anyone in the Advanced Molecular Manufacturing (AMM) community will recognize something like…

The tooltips themselves used for the deposition of carbon dimers were hammered on by the Q-SMAKAS (Quantum Search for Minimum Alternatives in Kinetically-Accessible Space) methodology (no, that wasn’t easy to make up), producing possible defect structures to explore how these tips might fall apart in an experimental apparatus. These tips were taken from the original survey paper [R. A. Freitas Jr., D. G. Allis and R. C. Merkle, "Horizontal Ge-Substituted Polymantane-Based C2 Dimer Placement Tooltip Motifs for Diamond Mechanosynthesis," J. Comput. Theor. Nanosci. 4, 433 (2007)] and the DC10c study [D. G. Allis and K. E. Drexler, "Design and Analysis of a Molecular Tool for Carbon Transfer in Mechanosynthesis," J. Comput. Theor. Nanosci. 2, 45 (2005) - and this one's available as a free download from HERE]. Much to my surprise, there’s a section of a book available for background on google: Tip-Based Nanofabrication: Fundamentals and Applications, by Ampere A. Tseng.

And for the non-AMM crowd, the same methodology of hammering on molecules in 3000 K to generate structural isomers can be employed at 300 K for the generation of conformational isomers, which was used to great success to explore the conformation-space of simple linear hydrocarbons and the far more interesting molecule biotin…

And Some Pick Hits From The Discussion

4.1 Unloaded Tooltips And Ge-Ge Bond Formation

Any stabilizing interactions within the open tooltip may serve to increase the barriers to structural rearrangement, H migration, etc. between the time a C2 dimer is deposited on a workpiece and the time the tooltip is recharged with a new C2 dimer.

4.2 More Stable Pathologies And Transition State Barriers

The identification of a more stable structure does not provide any insight into the energy barrier over which an operational mechanosynthetic geometry must pass in order to convert into a non-operational geometry.

Identifying from among the failure modes within some energy range which of the operational tooltip structures that are accessible within a thermal regime in a working system is a time-consuming but very important subsequent step in any continued developmental survey of these tooltips.

4.3 Hydrogen-Inverted Tooltip Geometries And Larger Tooltip Frameworks

These largely-ignored tooltip pathologies are the results of hydrogen inversion, a type of defect that finds one or more H atoms inserting into the cage framework as a result of a methodological mismatch of atom momentum and classical time step in the MD simulations … Three common workarounds for large H atom displacements per time step are (1) the use of smaller time steps to recalculate the forces on the H atoms, (2) the artificial increase of the mass of the H atoms to reduce their net displacement over some set time step (such as re-massing H atoms to deuterium or higher), and (3) the subsuming of the H atoms into the associated “heavy” atom to remove the H motion entirely from the simulation.

4.4 The NH@H Network And “Best-Practices” Considerations

The NH@H tooltip pathology survey generated a considerable amount of data and, after the analysis of the resulting data, yielded a selection of tooltip pathologies to serve as the basis for subsequent studies of tooltip defect pathways… The speed of a calculation and, ultimately, the quality of the calculation for a particular analysis are dictated by the quality of the computers owned by the participants… The use of a survey of representative available computers at the start of a series of quantum chemistry studies can be of great benefit in identifying the constraints a researcher must place on their investigation.

4.5 Identified Minima vs. Accessible Minima

In the absence of transition state calculations or MD simulations on larger tooltip frameworks to remove degrees of freedom in some atoms, it is not known how many of these tooltips can be ignored simply for energetic reasons — either due to large rearrangement barrier energies or due to one-step inaccessibility because of the presence of multiple barriers to complete a rearrangement to a predicted minimum.

4.6 Hydrogen Migration

In most stable tooltips, H migration is assumed to be the most accessible route to the formation of inoperative structures (what previous studies [R. A. Freitas Jr., D. G. Allis and R. C. Merkle, J. Comput. Theor. Nanosci. 4, 433 (2007)] have called “hydrogen poisoning”).

4.7 Ge-C Framework Bond Breaking

All of the tooltips in this study are designed to facilitate dimer deposition and tooltip retraction with the only modification to the covalent framework of the tooltip being the loss of the C2 dimer… The defects identified in the NH@H study with broken Ge-Cframework bonds may not themselves be accessible in isolation, but the additional bonding modes and resulting strain in the entire system as part of a mechanosynthetic operation makes such defect modes important in the overall design analysis of a diamondoid structure that is to be fabricated.

4.8 Combined Ge-C(framework) Bond Breaking And C=C π-Formation

The formation of broken Ge-C/C=C bond pathologies are noteworthy, both in the context of the operational issue described above and in the manner by which a symmetric bond breaking in these tooltips can produce very stable geometries that then require large transition state barriers to be present for the mechanosynthetic operability of the tooltip.

4.9 Ge-Ge Bond Formation

As noted in the Hydrogen Migration section, the formation of these strained bonds in the UT structures may not be detrimental to tooltip operation but may, by increasing the barrier to other defect modes, serve as a form of stabilization during the time between deposition and C2 dimer recharging.

4.10 C2 Positional Variation

Remarkably, despite the high temperatures and otherwise large deformations identified in many of the tooltip structures, specific structural deformations at the Ge-[C2 dimer]-Ge position were identified in only a few cases from the MD-based quantum chemistry optimizations… Here and generally, both the quality of the basis set and the inclusion of electron correlation (by way of the B3LYP density functional) are expected to make a considerable difference in the accuracy of the estimated relative energies.

4.11 Conformational Differences

In most rigid tooltip designs, the identification of conformational minima is interesting but otherwise not of significance, as conformational flexibility at the tooltip base is, like H inversion, removed from all structures as a result of embedding the structure within a larger and more constraining tooltip framework… This approach to tooltip design optimization via conformational control of the base has not been considered in previous studies and is one of the more interesting results to emerge from this initial NH@H study.

Additional Assorted

A few documents from the original website are reposted here in PDF format for historical purposes (providing a bit more context. If you were part of the original @Home crowd and participated in any of the forum discussions, all of the text above likely makes some amount of sense).

2011december10_NanoHive1andNanoHiveAtHome.pdf [download]

2011december10_QSMAKAS.pdf [download]

NanoHive-1 (NH1) is a modular simulator created by Brian Helfrich which is used for modeling the physical world at a nanometer scale. The intended purpose of the simulator is to act as a tool for the study, experimentation, and development of nanotech entities. NanoHive-1 is a GPL/LGPL licensed open-source development – you can download and use it for free. NanoHive-1 can be run stand-alone, or easily integrated to support other applications such as CAD tools.

NanoHive@Home (NHAH) is a distributed computing system also created by Brian Helfrich based on the BOINC platform that was used for large-scale nanotech systems simulation and analysis; drawing its computing power from otherwise idle computers sitting in people’s homes. The goal of NanoHive@Home was to perform large-scale nanosystems simulation and analysis that was otherwise too intensive to be calculated via normal means, and thereby enable further scientific study in the field of nanotechnology.

The Tooltip Failure Mode Search Project, conducted by Brian Helfrich and Dr. Damian Allis ran on NHAH from February 2007 through May 2007. It utilized computing cycles donated from over 6,000 computers worldwide and reached a peak performance of nearly 3 teraFLOPS. Here are links to the explanations and results of the project:

Explanation
Results

From the “free press” division of the blog, a recent post by Ferris Jabr on the scientificamerican.com site highlights yet another evolutionarily fascinating application of cyanocobalamin (herein referred to as B12) out of the Rob Doyle Lab for the non-invasive delivery of small molecules into the human-person. Here, a mechanism for the delivery of human peptide YY (hPYY) into the bloodstream via a food-free mechanism (unless you count the gum flavorings as a fruit). From the thorough and accessible article (with a decent balance of sciam and non-sciam redirecting)…

CHEMICAL COUPLE: The appetite-suppressing hormone hPYY hitches a ride with vitamin B-12 from the stomach to the bloodstream (caption credit: sciam).

Losing weight is not always about anticipating swimsuit season or squeezing into skinny jeans—for the clinically obese, losing weight is about fighting serious illness and reclaiming health. But the primal part of the brain that regulates appetite will not place a moratorium on hunger just because someone and their doctor acknowledge the need to lose weight. Researchers at Syracuse University are working toward a unique solution: a stick of chewing gum that suppresses appetite.

A slightly-larger version of the image on the site is reproduced above (with the image credit most welcome on the site). For a bit more information about the general properties of B12 and its potential applications for other diet-related issues, a few articles described here @swv link to more complete discussions…

* Vitamin B12 In Drug Delivery: Breaking Through The Barriers To A B12 Bioconjugate Pharmaceutical

* The Binding Of Vitamin B12 To Transcobalamin(II); Structural Considerations For Bioconjugate Design – A Molecular Dynamics Study

* B12-Insulin Bioconjugate/Transcobalamin(II)/Insulin Receptor Cover Image For The April Issue Of Clinical Chemistry

* New B12-Insulin-TCII-Insulin Receptor Cover Image For This Month’s ChemMedChem (March 2009)

* Exploring the Implications of Vitamin B12 Conjugation to Insulin on Insulin Receptor Binding and Cellular Uptake

It seems a near-impossibility that you can buy something in a store today that has (as of this post) ZERO google footprint, but I found it. On a recent trip to Buke at the Music Center on James St., I picked up the cymbal/chime/bell/thing below. The only identifiers on this 6″ core of a heavy ride cymbal are the cursive TM’ed text that looks like “Zenero” and a pure tone that can be easily discerned from background noise for a minute or more (and you can feel the air buzzing just around it as it rings).

A post to the drummerworld forum (drummerworld.com/forums/showthread.php?t=84143) simply confirmed my attempts to find info about this thing, making the drummerworld post and this blog currently “it” for info, which remains either the best or worst marketing gimmick on the internets today, with my suspicion still leaning to the former.

And, furthermore, speaking of cymbals, I bought this around the same time the planet lost one of the great independent cymbal makers in Roberto Spizzichino.