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Computational biochemistry and biophysics 1st Edition Oren M. Becker
Computational biochemistry and biophysics 1st Edition
Oren M. Becker Digital Instant Download
Author(s): Oren M. Becker, Alexander D. MacKerell Jr., Benoit Roux,
Masakatsu Watanabe
ISBN(s): 9780824704551, 082470455X
Edition: 1st
File Details: PDF, 5.33 MB
Year: 2001
Language: english
Computational biochemistry and biophysics 1st Edition Oren M. Becker
Computational biochemistry and biophysics 1st Edition Oren M. Becker
ISBN: 0-8247-0455-X
This book is printed on acid-free paper.
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Foreword
The long-range goal of molecular approaches to biology is to describe living systems in
terms of chemistry and physics. Over the last 70 years great progress has been made in
applying the quantum mechanical equations representing the underlying physical laws to
chemical problems involving the structures and reactions of small molecules. This work
was recognized in the awarding of the Nobel Prize in Chemistry to Walter Kohn and John
Pople in 1998. Computational studies of mesoscopic systems of biological interest have
been attempted only more recently. Classical mechanics is adequate for describing most
of the properties of these systems, and the molecular dynamics simulation method is the
most important theoretical approach used in such studies. The first molecular dynamics
simulation of a protein, the bovine pancreatic trypsin inhibitor (BPTI), was published
more than 20 years ago [1]. Although the simulation was ‘‘crude’’ by present standards,
it was important because it introduced an important conceptual change in our view of
biomolecules. The classic view of biopolymers, like proteins and nucleic acids, had been
static in character. The remarkable detail evident in the protein crystal structures available
at that time led to an image of ‘‘rigid’’ biomolecules with every atom fixed in place [2].
The molecular dynamics simulation of BPTI was instrumental in changing the static view
of the structure of biomolecules to a dynamic picture. It is now recognized that the atoms
of which biopolymers are composed are in a state of constant motion at ordinary tempera-
tures. The X-ray structure of a protein provides the average atomic positions, but the atoms
exhibit fluidlike motions of sizable amplitudes about these averages. The new understand-
ing of protein dynamics subsumed the static picture in that the average positions are still
useful for the discussion of many aspects of biomolecule function in the language of
structural chemistry. The recognition of the importance of fluctuations opened the way
for more sophisticated and accurate interpretations of functional properties.
In the intervening years, molecular dynamics simulations of biomolecules have un-
dergone an explosive development and been applied to a wide range of problems [3,4].
Two attributes of molecular dynamics simulations have played an essential role in their
increasing use. The first is that simulations provide individual particle motions as a func-
tion of time so they can answer detailed questions about the properties of a system, often
more easily than experiments. For many aspects of biomolecule function, it is these details
iii
iv Foreword
that are of interest (e.g., by what pathways does oxygen get into and exit the heme pocket
in myoglobin? How does the conformational change that triggers activity of ras p21 take
place?). The second attribute is that, although the potential used in the simulations is
approximate, it is completely under the user’s control, so that by removing or altering
specific contributions to the potential, their role in determining a given property can be
examined. This is most graphically demonstrated in the calculation of free energy differ-
ences by ‘‘computer alchemy’’ in which the potential is transmuted reversibly from that
representing one system to another during a simulation [5].
There are three types of applications of molecular dynamics simulation methods in
the study of macromolecules of biological interest, as in other areas that use such simula-
tions. The first uses the simulation simply as a means of sampling configuration space.
This is involved in the utilization of molecular dynamics, often with simulated annealing
protocols, to determine or refine structures with data obtained from experiments, such as
X-ray diffraction. The second uses simulations to determine equilibrium averages, includ-
ing structural and motional properties (e.g., atomic mean-square fluctuation amplitudes)
and the thermodynamics of the system. For such applications, it is necessary that the
simulations adequately sample configuration space, as in the first application, with the
additional condition that each point be weighted by the appropriate Boltzmann factor. The
third area employs simulations to examine the actual dynamics. Here not only is adequate
sampling of configuration space with appropriate Boltzmann weighting required, but it
must be done so as to properly represent the time development of the system. For the first
two areas, Monte Carlo simulations, as well as molecular dynamics, can be utilized. By
contrast, in the third area where the motions and their development are of interest, only
molecular dynamics can provide the necessary information. The three types of applica-
tions, all of which are considered in the present volume, make increasing demands on the
simulation methodology in terms of the accuracy that is required.
In the early years of molecular dynamics simulations of biomolecules, almost all
scientists working in the field received specialized training (as graduate students and/or
postdoctoral fellows) that provided a detailed understanding of the power and limitations
of the approach. Now that the methodology is becoming more accessible (in terms of
ease of application of generally distributed programs and the availability of the required
computational resources) and better validated (in terms of published results), many people
are beginning to use simulation technology without training in the area. Molecular dynam-
ics simulations are becoming part of the ‘‘tool kit’’ used by everyone, even experimental-
ists, who wish to obtain an understanding of the structure and function of biomolecules.
To be able to do this effectively, a person must have access to sources from which he or
she can obtain the background required for meaningful applications of the simulation
methodology. This volume has an important role to play in the transition of the field
from one limited to specialists (although they will continue to be needed to improve the
methodology and extend its applicability) to the mainstream of molecular biology. The
emphasis on an in-depth description of the computational methodology will make the
volume useful as an introduction to the field for many people who are doing simulations
for the first time. They will find it helpful also to look at two earlier volumes on macro-
molecular simulations [3,4], as well as the classic general text on molecular dynamics
[6]. Equally important in the volume is the connection made with X-ray, neutron scatter-
ing, and nuclear magnetic resonance experiments, areas in which molecular dynamics
simulations are playing an essential role. A number of well-chosen ‘‘special topics’’ in-
volving applications of simulation methods are described. Also, several chapters broaden
Foreword v
the perspective of the book by introducing approaches other than molecular dynamics for
modeling proteins and their interactions. They make the connection with what many peo-
ple regard—mistakenly, in my view—as ‘‘computational biology.’’ Certainly with the
announced completion of a description of the human genome in a coarse-grained sense,
the part of computational biology concerned with the prediction of the structure and func-
tion of gene products from a knowledge of the polypeptide sequence is an important
endeavor. However, equally important, and probably more so in the long run, is the bio-
physical aspect of computational biology. The first set of Investigators in Computational
Biology chosen this year demonstrates that the Howard Hughes Foundation recognized
the importance of such biophysical studies to which this volume serves as an excellent
introduction.
I am very pleased to have been given the opportunity to contribute a Foreword to
this very useful book. It is a particular pleasure for me to do so because all the editors
and fifteen of the authors are alumni of my research group at Harvard, where molecular
dynamics simulations of biomolecules originated.
REFERENCES
1. JA McCammon, BR Gelin, and M Karplus. Nature 267:585, 1977.
2. DC Phillips. In: RH Sarma, ed. Biomolecular Stereodynamics, II. Guilderland, New York: Ade-
nine Press, 1981, p 497.
3. JA McCammon and S Harvey. Dynamics of Proteins and Nucleic Acids. Cambridge: Cambridge
University Press, 1987.
4. CL Brooks III, M Karplus, and BM Pettitt. Proteins: A Theoretical Perspective of Dynamics,
Structure, and Thermodynamics. New York: John Wiley & Sons, 1988.
5. For an early example, see J Gao, K Kuczera, B Tidor, and M Karplus. Science 244:1069–1072,
1989.
6. MP Allen and DJ Tildesley. Computer Simulations of Liquids. Oxford: Clarendon Press, 1987.
Martin Karplus
Laboratoire de chimie Biophysique, ISIS
Université Louis Pasteur
Strasbourg, France
and
Department of Chemistry and Chemical Biology
Harvard University
Cambridge, Massachusetts
Computational biochemistry and biophysics 1st Edition Oren M. Becker
Preface
The first dynamical simulation of a protein based on a detailed atomic model was reported
in 1977. Since then, the uses of various theoretical and computational approaches have
contributed tremendously to our understanding of complex biomolecular systems such
as proteins, nucleic acids, and bilayer membranes. By providing detailed information on
biomolecular systems that is often experimentally inaccessible, computational approaches
based on detailed atomic models can help in the current efforts to understand the relation-
ship of the structure of biomolecules to their function. For that reason, they are now
considered to be an integrated and essential component of research in modern biology,
biochemistry, and biophysics.
A number of books and journal articles reviewing computational methods relevant
to biophysical problems have been published in the last decade. Two of the most popular
texts, however, were published more than ten years ago: those of McCammon and Harvey
in 1987 and Brooks, Karplus, and Pettitt in 1988. There has been significant progress in
theoretical and computational methodologies since the publication of these books. There-
fore, we feel that there is a need for an updated, comprehensive text including the most
recent developments and applications in the field.
In recent years the significant increase in computer power along with the implemen-
tation of a wide range of theoretical methods into sophisticated simulation programs have
greatly expanded the applicability of computational approaches to biological systems. The
expansion is such that interesting applications to important and complex biomolecular
systems are now often carried out by researchers with no special training in computational
methodologies. To successfully apply computational approaches to their systems of inter-
est, these ‘‘nonspecialists’’ must make several important choices about the proper methods
and techniques for the particular question that they are trying to address. We believe that
a good understanding of the theory behind the myriad of computational methods and
techniques can help in this process. Therefore, one of this book’s aims is to provide readers
with the required background to properly design and implement computational investiga-
tions of biomolecular systems. In addition, the book provides the needed information for
calculating and interpreting experimentally observed properties on the basis of the results
generated by computer simulations.
vii
viii Preface
This book is organized so that nonspecialists as well as more advanced users can
benefit. It can serve as both an introductory text to computational biology, making it useful
for students, and a reference source for active researchers in the field. We have tried
to compile a comprehensive but reasonably concise review of relevant theoretical and
computational methods that is self-contained. Therefore, the chapters, particularly in Part
I, are ordered so that the reader can easily follow from one topic to the next and be
systematically introduced to the theoretical methods used in computational studies of bio-
molecular systems. The remainder of the book is designed so that the individual parts as
well as their chapters can be read independently. Additional technical details can be found
in the references listed in each chapter. Thus the book may also serve as a useful reference
for both theoreticians and experimentalists in all areas of biophysics and biochemical
research.
This volume thus presents a current and comprehensive account of computational
methods and their application to biological macromolecules. We hope that it will serve
as a useful tool to guide future investigations of proteins, nucleic acids, and biological
membranes, so that the mysteries of biological molecules can continue to be revealed.
We are grateful to the many colleagues we have worked with, collaborated with,
and grown with over the course of our research careers. The multidimensionality of those
interactions has allowed us to grow in many facets of our lives. Special thanks to Professor
Martin Karplus for contributing the Foreword of this book and, most important, for supply-
ing the insights, knowledge, and environment that laid the foundation for our scientific
pursuits in computational biochemistry and biophysics and led directly to the creation of
this book. Finally, we wish to acknowledge the support of all our friends and family.
Oren M. Becker
Alexander D. MacKerell, Jr.
Benoı̂t Roux
Masakatsu Watanabe
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Harper and myself, and soon we had the tent pitched and were snug
for the night.
At three o’clock on the Saturday morning Dixon and I crawled out
of our sleeping-bags, and by 4 a.m. we were on the snow slopes,
determined to make a vigorous attack upon the peak which had so
long defied us.
Two hours on fairly good snow slopes and a scramble over a nasty
slab-like face of rock, and once again the plateau, and that glorious
scene of Aorangi and Tasman, were before us.
But the wind had risen quickly and was blowing a gale from the
south-west—the cold quarter. To face such a wind for any length of
time, or to attempt to climb Aorangi against it, would be simple
madness, so we turned and ignominiously fled to the refuge of our
bivouac, 1,200 feet below, which we reached at seven o’clock,
having been but three hours absent.
We then sent Annan down, as we were keeping him from his work
in the lower country, telling him to leave word with the survey party
that if we did not arrive back at the Ball Glacier by Monday night
something would probably have gone amiss with us.
During the day the gale blew itself out, and next morning at 3.45
we were in our steps of the day before, reaching the plateau in an
hour and a half. The morning sun lit up the peaks with a rosy glow,
soon his piercing beams forced us to put on the goggles, while the
crust of the snow began to soften under the great power of
penetration which the rays possess in the rarefied air. This forced us
to plod onward in slushy snow as we headed right for the Linda
Glacier, which we could see rounding the point of the north-eastern
arête of our mountain.
On our right rose Mount Tasman clothed in ice, from which during
the night an immense avalanche had descended. We walked close to
its furthest point of motion as it lay stretched out on the level snow-
field like a gigantic breakwater, and found it to be 300 paces in
width; Dixon estimated that it covered from forty to fifty acres.
We now put on the rope, as crevasses began to appear in the
gently rising slopes to the Linda Glacier. On our left we thought that
the north-eastern ridge looked practicable, but deemed it better to
rely on a route chosen by so able a mountaineer as Ulrich
Kaufmann, and kept on our course for the Linda Glacier, taking ten-
minute spells at leading and breaking steps in the soft and slushy
snow, and winding our way amongst ever-increasing crevasses in
search of snow bridges over which we would cautiously crawl.
Now we would have a stretch of gently rising snow, then a
crevasse or perhaps a bergschrund, followed by a steep ascent for
100 or 200 feet, then a divergence to one side or the other to avoid
a chaos of séracs or blocks of tumbled and broken ice; and so on,
hour after hour. About noon we had gained a considerable elevation
above the plateau and were well round the corner on the Linda
Glacier. Into this elevated valley the sun poured down through a
rarefied atmosphere on to slopes on either hand which reflected all
the light and heat. The glare was something dreadful, and before
midday our faces and hands had assumed the customary chocolate
colour, and the skin was literally broiled off me; Dixon did not suffer
to such an extent. The heat was most intense, though not of the
enervating kind which one feels at lower altitudes.
Viewed from this quarter Aorangi presents a totally different form
than from any other, and we began to be sanguine about
accomplishing our task. I was in possession of notes and sketches of
the route kindly sent me by Mr. Green, and these were of material
assistance to us.
Before us lay the final peak with its capping of ice. From the
summit, now in full view, descended in a north-westerly direction to
the right a steep rocky arête connecting with the ridge leading on to
Mount Tasman. From the lower parts of these rocks steep ice slopes
streaked with marks from falling rocks descend to the upper portions
of the Linda Glacier, bounded all along their lower termination by an
immense bergschrund which severs them from immediate contact
with the glacier itself.
On the left of the summit slopes the north-eastern arête,
consisting of a ridge of alternate knife-edges of ice and gensdarmes
or towers of rock. The northern side or face of this ridge descending
to the Linda Glacier is composed of very steep slopes of ice set with
three immense masses of red sandstone rocks, with two ice-filled
couloirs or ditches between them. Up these two couloirs lay our
route. We thought, however, that by leaving the glacier and taking to
the crest of the ridge we could improve on the route, but soon found
that the change was a mistake, and so struck back on to our old
course up the middle of the glacier, the final slopes of which were
very steep and exposed to the chance of avalanches from either
hand.
It seemed a hopeless task this plunging through soft snow hour
after hour, and it was nearly one o’clock ere we gained the edge of
the big bergschrund and with difficulty discovered a sound enough
snow bridge. Shortly before this an incident occurred in crossing one
of these snow bridges which brought forcibly before our minds the
serious nature of the work in which we were engaged. I—the lighter
man by two stone—had crawled over in safety, and planting myself
well in the soft snow above, was taking in the slack of the rope as
Dixon followed, when suddenly he went through up to his armpits
and was dangling in space, held up by a thin crust of snow and by
the rope from above. I pulled with the strength of despair, and Dixon
struggled till he secured a hold somehow on the other lip of the
crevasse and got out.
That sort of thing is all very well to look back upon and talk over
afterwards, but I am not likely to forget for many a long day the
sensation of holding up a thirteen-stone man under such
circumstances, and I must say that I should have been much easier
in my mind if we had had such a man as Emil Boss or Ulrich
Kaufmann on one end of the rope.
Immediately after crossing the big bergschrund step-cutting
commenced; and from this point upwards every step, other than
those on rocks, had to be cut in hard ice.
It is no easy task after climbing steadily for nine hours in soft
snow to set to work and cut steps, especially when one knows that a
slip must on no account be made, for with two men only on the rope
it would mean a sudden descent to the crevasses or precipices (as
the case may be) below, and our certain destruction.
An hour’s steady work and we gained the foot of the lowest rocks,
which were found to be quite unscalable. We then sidled round the
base of these rocks to the left and commenced cutting steps up the
first couloir, keeping close into the rocks on our right, on which we
could get an occasional hand-grip. Ice blocks were continually
coming down from the broken masses overhanging the top of the
couloir, but luckily none struck us. The descent of an ice block in
such steep ice slopes is something to remember. First a rattle above,
and then ‘swish, swish’ as the first leaps begin, followed by a ‘whir-r-
r-r’ and a ‘hum-m-m-m’ as, like a flash of light, a spinning and
ricochetting object goes by and is lost to sight over the brink of the
precipice below, or perchance is detected spending its momentum
on the soft snow slopes 1,000 feet down.
These falls of ice on the upper slopes are not like the hissing
avalanches, which sometimes even crawl down the lower snow
slopes, but come down with the speed of light, and are calculated to
strike terror into the heart of the stoutest-nerved climber.
We crossed the couloir near its head, partly on ice and partly on
rocks, amid the gravest peril from showers of ice, and took to the
rocks on our left, which were both dangerous and difficult, mainly
owing to their being here and there coated with ice. Soon they
became quite inaccessible, and we were again forced towards our
left on to the ice slopes in the second couloir, and here we found the
ice even harder, and we could only make an impression on it with
the spike end of our axes. To add to the difficulty, the angle of
ascent became steeper, inclining in places to about 60° from the
horizontal.
We negotiated this couloir in a similar manner to that below, but
water trickling from the overhanging rocks formed awkward
hummocks of ice on the slope close to the rocks, over which we
thought it almost impossible to climb, and to go out into the middle
of the couloir was impossible, owing to falling ice.
Time was quickly passing, and we had a terrible fight to reach the
head of the couloir. The rocks now shaded us from the sun’s rays,
and soon our hats, coats, and the rope were frozen as stiff as
boards, while the cold was so intense as to cause the skin of our
hands to adhere to the steel of the ice-axes.
It seemed now more than ever a hopeless task to reach the final
ice-cap, which we knew could not be far above us; but we silently
and doggedly cut away, and at length were rewarded by finding the
rocks on our right practicable; taking to them we were soon on their
crest, and the ice-cap of the mountain lay straight before us. An
easy bit of rock-climbing led up to the slopes, which we found to be
covered with a peculiar form of lumpy and frozen drifted snow. At
the top of the rocks we looked around in vain for Mr. Green’s cairn,
with his handkerchief and Kaufmann’s matchbox, left on the
occasion of their ascent in March 1882. Doubtless they have either
been long since swept away by falling ice or were buried in the
terminal of the ice slope, which in December would encroach farther
down upon the rocks than in March.
Dixon now counselled a retreat, arguing that we had virtually
overcome all the difficulties and had only the final and easy slope to
cut up; but I persuaded him to stay a little longer and make a push
for it, or at least as much of a push as we were capable of making.
AORANGI: THE HIGHEST PEAK
[From a Water-colour Sketch
It was half-past five. Four hours and a half we had been toiling
from the head of the Linda Glacier, thirteen hours and a half from
our bivouac, without any halt to speak of. A wind began to blow
from the north-west, adding fresh cause for anxiety about the
descent. One thing was certain—if we wanted to get down alive we
should have to reach the Linda Glacier again before dark.
We worked as hard as we were able at step-cutting for another
fifteen minutes, but only made slow progress; yet there was the
cornice, just away to the right, the crest of the ridge to the left, and
the top scarcely a stone’s throw above, with no difficulty in the way.
What would we not have given for another hour of daylight? How
could we turn away when so near to a complete victory over our old
foe?
Dixon again suggested turning, and I could not do otherwise than
defer to his advice, for already we were caught in a trap, and should
bad weather come upon us—and the wind and cold were fast
increasing—before we reached the Linda Glacier again the
probabilities were that we never should have returned from the
giddy heights of the great Aorangi, the ‘Sky-piercer.’
The height of the mountain is 12,349 feet; our aneroid read at our
turning-point 12,300, and we reckoned the summit to be 140 feet
above us. The slight error in the reading of the instrument would be
accounted for by the impending change of weather.
The view is magnificently comprehensive. Looking northwards we
could see clear over the top of our giant neighbour, Mount Tasman
(11,475 feet). On the western side, the ocean, but twenty miles
distant, was covered by a mantle of low-lying clouds creeping into
the bays and inlets of the coast, studded here and there with
islanded hill-tops, and stretching away to what seemed a limitless
horizon on the west. A streak of blue ocean showed through the
cloud mantle near Hokitika, seventy miles northwards.
North-eastwards the glorious array of the Southern Alps extended,
presenting a panorama of such magnificence and
comprehensiveness that it defies any attempt at description. It is
one of those vast pictures which are indelibly impressed upon the
memory—one of those overpowering examples of Nature’s sublimity
which seem to move a man’s very soul and call him to a sense of his
own littleness.
Close under us lay the scenes of all our joys and sorrows of the
past five years: the Tasman Glacier, encircled by those splendid
peaks and snow-fields whose forms we had learned to know and
love so well; further afield lay the Liebig Range, and, showing over
this, Mount Jukes and his attendant satellites of rocky peaks. Beyond
this again, far, far away in the blue and indefinite east, we could
distinguish the hills of Banks Peninsula, close to our homes near
Christchurch, whilst we could imagine that the blue haze
distinguishable there was indeed the eastern ocean, 120 miles
distant.
It will, of course, be said that we did not make the complete
ascent of the mountain. Be that so; neither does Mr. Green claim
that honour, though for all practical purposes to be on the ice-cap of
Aorangi means the same thing as being on the top. Mr. Green’s
highest point must, according to his sketches, have been as nearly
as possible 100 feet above ours.
But we could not spare time to moralise and rest as we should like
to have done, for it was imperative that the terrible ice slopes should
be descended before the light failed, and at a few minutes to six we
began to go down backwards in our steps, taking a firm hold with
our axes at every step.
This going down is a fearful strain on the nerves, and requires the
greatest steadiness and caution. In hurrying down the easy rocks we
missed a mark on a snow patch which Dixon had made to denote
the right route, and this mistake at the outset caused us nearly half
an hour’s delay before we found the right spot from which to leave
the crest of the rocks. Dixon led down the rocks and I followed,
every now and then taking a turn round any prominent projection
with the rope and easing him down, whilst he in turn secured a good
hold and took in the slack as I came down.
Bad as it had been coming up the top couloir, it was infinitely
worse going down, for what was trickling water on the upward
journey was now solid ice, and many of the steps were filled with re-
frozen chips of ice from the steps we had cut above, and these had
to be cleaned out before we could get a secure foothold.
Cutting steps up is one thing, and cutting them down another, for
on a steep slope one cannot turn round face downwards to get at
one’s work, which in the case of going up-hill lies convenient to the
hand.
How we did get down without the fatal slip which I was
momentarily expecting would be made by one or the other of us I
never could quite understand.
The rocks below the topmost couloir were negotiated and the
lower couloir reached. This was not so difficult to descend, and the
effect of the frost was such as to prevent such a continual shower of
ice blocks from above, thus minimising one prominent danger.
The lower parts of the couloir were reached, and here are situated
the rocks which form the ledge upon which with Boss and Kaufmann
Mr. Green stood out for the night. There are several ledges
accessible, but Mr. Green’s party must have been upon one of the
higher, for on some of the lower ledges there is room for a dozen
men to stand or even lie down, though scarcely space enough for a
circus or Wild West show, as Dixon humorously suggested. The light
was now fast failing, and we strained every nerve to reach the big
bergschrund below before darkness was upon us.
We were just in time and that was all, and the frail snow bridge
was passed by our sliding over on our backs; I, the lighter man, led,
and Dixon followed as steady as a rock—not a Mount Cook Rock, but
the proverbial one.
We had now been seventeen hours with every nerve and muscle
constantly in action, and yet, as the darkness set in and the awful
glare of the sun had left us, we began to freshen up, and lighting
one of our Austrian climbing-lanterns we retraced our footsteps of
the morning, being most careful never to deviate from them. Soon it
became very dark, for there was no moon, and we could but dimly
distinguish the ghostly forms of the white-robed peaks which shut us
in on all hands.
Hour after hour we plodded on. On one occasion we were brought
up by the crevasse into which Dixon had nearly fallen in the
morning; it had opened wider during the day, and only after walking
along its line of fracture in both directions for half an hour did we
discover a bridge which seemed sufficiently strong. We crossed in
our usual way, sliding over at full length, and putting some weight
on to our axe-handles laid lengthways on the snow to distribute the
weight as much as possible.
As the night wore on, the crust of the snow became harder, and
after passing through that most unpleasant crusted stage when it
will bear until all the weight is put on one foot, became quite
pleasant to walk upon, and over the lower part of the Linda Glacier
and across the plateau we made a fair pace. As we reached the rise
off the plateau on to the Haast Ridge the wind increased in violence,
and we had great difficulty in keeping our lanterns (two of which we
now kept going) alight.
The crest of the ridge was gained, and the descent of the
dangerous snow slopes to the bivouac, 1,200 or 1,400 feet below,
commenced. We were soon in trouble again amongst bergschrunds
and crevasses, and on two occasions, in going down and feeling for
the next step behind, I found on showing a light that my hind leg
was dangling in a crevasse!
I must not weary you, dear reader, with further monotonous
descriptions of crossing these deadly enemies of the mountaineer,
suffice it to say that after an exasperating hunt on the steep slopes
and in the dark for our bivouac—the candles being just finished—we
finally discovered it at 2.45 a.m., an hour before daylight, having
been twenty-three hours constantly hard at work without any halt
worthy the name.
Sleeping soundly till 9 a.m. we made up our swags, and by 11 a.m.
were on the downward route again for the Ball Glacier camp.
It was quite a wrench to leave our friendly rock, which had
become a haven of rest and refuge to us on this upper beat. Five
nights have I spent under its protection at different times, and as
often have I arisen with the early morn to gaze upon those vast and
sublime solitudes of Nature so grandly unfolded to view. From this
little home—out of which if one stepped one had to be careful not to
lose one’s footing and make a rapid descent to the Hochstetter
Glacier on one hand or to the Freshfield on the other—I have seen
the rosy tints of the newly-born day creep downwards from the
hoary snow-caps of the mountains, and when evening drew on have
watched the afterglow envelop all in its warm embrace, even black
rocks turning to a deep crimson which seemed to pervade the higher
peaks ere the black and cold night once again grasps them in his icy
hold.
Here had tired limbs been laid to rest whilst wearied minds
dreamed dreams of success and hope, gaining renewed vigour with
the morning light to go forth afresh into new struggles and
enjoyments. Here in the heart of great Nature’s solitudes the
thoughts flew back to homes of comfort and of love. What wonder
that we should have formed associations with such a spot?
The Ball Glacier camp was reached at 4.30 p.m., where we found
Mr. Sladden of the Survey party anxiously awaiting our arrival, with
that forethought which shows the kindly feeling and consideration
for others that characterises men of worth in these outlandish parts.
That evening Dixon went across with Sladden to the Survey camp
in the Murchison Valley, leaving me to wait for an expected friend
from Christchurch.
Here I was quite alone amongst the mountains, with plenty of
time to muse over the events of the past few days and to let my
wandering thoughts fly back even further, to the struggles of the
past five years whilst attempting to conquer Aorangi.
What is the climber’s reward for all his trouble? Why does he
climb? Who can tell?
Is it renown he struggles for? No; I am convinced that is a very
infinitesimal motive. For mercenary ends? No; there is no financial
harvest to reap.
I have often tried to think why men undergo such labour and
hardship, but cannot come to any definite conclusion. To overcome
set tasks (‘pure cussedness’ the Americans would say) is one reason
(after once putting one’s hand to the plough). To gain physical and
mental strength, to raise and purify the mind in Nature’s great
school, are both potent reasons. But, above all, there is some
mysterious influence pervading all true mountaineers—a mountain
fever, a close kinship with Nature (call it what you will), a hidden
impulse that grows on a man who has once felt what it is to taste
the sweets of climbing and to enjoy the fascinations of the world
above the snow-line.
My friend did not arrive, so I made my way over to Mr. Brodrick’s
Survey camp on the Murchison, walking through a thick mist, and
steering across the Tasman by the aid of a compass—a distance of
seven miles, or three hours’ walking from camp to camp.
Here I found Cooper—Messrs. Wheeler & Son’s photographic
operator—who was down securing views of the district for a lecture
which I was to deliver before the Australasian Association for the
Advancement of Science.
It was our intention to make a two days’ excursion up the
Murchison Glacier with Cooper, but showery weather put a veto on
our plans, and we were fain to be content with a short excursion to
the Onslow Glacier, where some exposures were effected.
Leaving Mr. Brodrick’s hospitable quarters on December 10, by the
12th we were again at the Hermitage.
Computational biochemistry and biophysics 1st Edition Oren M. Becker
CHAPTER X
ON SOME OF THE PHENOMENA OF GLACIERS,
WITH SPECIAL REGARD TO THOSE OF NEW
ZEALAND
The cause of glaciers—Formation and structure—
Motion—Moraines: Lateral, medial, and terminal
—‘Surface’ moraines—Crevasses—Moulins—Glacier
cones—Glacier tables—Surface torrents—
Avalanches—Cornices
In a work of this nature it may not be out of place to briefly describe
some of those interesting features and phenomena which
accompany the world above the snow-line.
Here is a quotation from a recent review of Professor Heim’s
work[2] by a prominent member of the English Alpine Club:—
‘Some thirty years ago a systematic résumé of all that was known
up to that date about existing glaciers appeared in the work of
Professor Albert Mousson, “Die Gletscher der Jetztzeit,” since which,
with perhaps the exception of Major Hüber’s “Les Glaciers,” no
attempt has been made to collect into a focus the light which
numerous able observers and theorists have subsequently thrown
upon the question. The intricacy of the problem has, indeed,
increased almost in proportion to our enlarged knowledge of its
conditions; and in spite of the labours of a large and very
distinguished body of investigators, not only do many important
points remain matters of dispute, but the very materials for a
complete solution are still wanting.’
[2] Handbuch der Gletscherkunde, von Dr. Albert Heim, Zürich
(Stuttgart: Verlag von J. Engelhorn, 1885, 18 francs.)
CAUSE OF GLACIERS
The joint cause of glaciers is precipitation and cold. A low
temperature alone can do nothing without moisture, and this fact
quickly disposes of the popular notion that glaciers invariably exist in
cold countries. Thibet, for instance, and also some parts of Arctic
North America are destitute of ice streams, though eternal cold may
be said to reign supreme in these parts.
Imagine for a moment the higher mountains clear of snow and
ice, and then watch for the formation of a glacier. Snow falls and fills
up all the valleys and gullies, avalanches descend from the higher
parts, and a great accumulation gathers in all hollows. By constant
repetition of snow-falls (always provided a greater quantity is
deposited than can be melted by the sun’s rays and by the natural
warmth of the earth’s crust) great pressure is put upon the lower
portions by the superincumbent accumulation, and aided by the
infiltration of water and refreezing (or ‘regelation’ as the correct term
is), a large body of ice is formed which at once begins to move down
the valleys containing it.
GLACIER ICE
Glacier ice is not like the solid blue ice on the surface of water, but
consists of granules joined together by an intricate network of
capillary water-filled fissures.
In exposed sections and upon the surface of the ice can be
observed a ‘veined’ or ‘banded’ structure—veins of a denser blue
colour alternating with those of a lighter shade containing air
bubbles.
The cause of this peculiar structure has been the subject of much
theorising amongst investigators, but hitherto I believe the greatest
authorities consider that the explanation of the phenomenon is yet
wanting.
GLACIER MOTION
The motion of glaciers is yet another bone of contention, but it is
generally admitted that the cause of it is to be found mainly in
gravitation, and is also partially accounted for by the strange
property of ‘viscosity’ in what appears to the casual observer to be
nothing more or less than a rigid solid.
Recently observations for ascertaining the rate of progress of the
Tasman, Murchison, Hooker, and Mueller Glaciers have been made
by the New Zealand Government Survey Department. Some of the
results were embodied in a paper by Mr. J. H. Baker, the Chief
Surveyor of the Provincial District of Canterbury, and will appear in
the ‘Transactions of the Australasian Association for the
Advancement of Science’ for 1891. At the late meeting of that body
a committee was appointed to further these investigations, and a
sum of 25l. voted for the aid of the same.
Before long, therefore, there will be put before the scientific public
reliable measurements of the motion of several of the largest and
least-known glaciers in temperate regions.
MORAINES
There is a remarkable feature of the glaciers of this country which
stamps them as unique in one respect—I refer to the very extensive
moraines. I write feelingly of this, for my acquaintance with them
has been a very close one, and they have impressed me very deeply
—in more ways than one.
The large glaciers of which I have written in this work are
completely moraine-covered over their lower parts.
‘SURFACE’ MORAINES
Moraines may be divided into four sections: ‘Lateral’ moraines,
fringing the sides of the glaciers, their outlying portions often being
‘dead’—that is, at present unmoved by the action of the ice, and
forming banks, as it were, for the ice stream to flow between;
‘medial’ moraines, which begin at the junction of two streams of ice
and often continue for many miles to the terminal face; ‘terminal’
moraines, formed by the depositing of detritus at the melting point
or end of the glacier; and, lastly, ‘surface’ moraines (so called by
Professor Hutton of Christchurch, N.Z.), which are the combined
accumulations of the first two divisions in the lower parts of the
glacier.
It is these ‘surface’ moraines that are such a characteristic feature
of the glaciers situate on the eastern side of the chain in New
Zealand. Of those on the western side I am not able to speak with
authority, never having visited them myself; but I understand that
they do not carry such a large quantity of detritus as those of the
eastern slopes.
This disparity remains to be accounted for and awaits an
explanation. I have a theory of my own upon the subject, which,
however, as yet I would not like to put too strongly forward.
On both sides of Mount Cook, on Mount De la Bêche (ten miles
further along the chain), and on a peak just north of the Hochstetter
Dome (ten miles still further north) I have observed enormous
exposed sections of the rock strata, which in each case dip at a
steep angle from east to west, presenting slab faces, not easily
disturbed by the action of the frost, to the westward, but broken and
fast denuding faces (‘basset’ faces, as they are geologically termed)
to the eastward. I am hoping at some future time to further
investigate this interesting subject.
As the western glaciers, however, must descend steeper valleys
than the eastern, I make no doubt that their rate of progress will be
eventually ascertained to be greater than that of the latter, and this
would militate largely against an accumulation of moraine upon the
ice.
THE SURFACE OF A GLACIER
All sorts of queer notions as to what the surface of a glacier is like
exist. Indeed I have often heard people inquire if it would be
possible to skate upon it!
Let us for a moment imagine ourselves at the head of the great
Tasman Glacier, 8,600 feet above sea-level. All around us is snow,
either freshly fallen or merging into névé. We begin to walk down,
and at first, upon the steeper slopes, cross a few large crevasses
and bergschrunds by means of snow bridges; then, as the incline
becomes less steep, we walk for six miles or so upon a smooth
surface of névé, or perchance knee-deep in fresh snow, and scarcely
a crevasse exists. At the beginning of the great turn we gradually
leave the névé and find ourselves upon hard, white ice, and soon
transverse crevasses appear; these are a little further on cut by
longitudinal crevasses forming the surface into huge squares, not flat
on the top, but hummocky. A perfect network of crevasses cuts up
the whole of the surface, but those parts on the outside of the curve
are infinitely more disturbed than those on the inside, owing to the
tension put upon them by the faster rate at which they have to
move. After rounding the turn the glacier again consolidates and few
crevasses appear, only the surface is covered with old wounds—if I
may coin such a term—from the rents which have occurred at the
turn, and presents a very undulating appearance. The little gullies
are formed into watercourses and intersect the glacier in all
directions. On our right, now, is the medial moraine formed by
detritus from Mount De la Bêche, brought down partly by the
Tasman and partly by the Rudolf Glaciers, and it stands up 100 feet
or so above the surface of the clear ice on either side of it, owing to
the protection from the sun’s rays afforded by it to the ice beneath,
so preventing ‘ablation’ or waste going on so quickly. We follow
down for another four or five miles, and then cross this moraine
(which has in the meantime joined that on the northern side of the
Hochstetter Glacier) on to the Hochstetter on our right.
SURFACE TORRENTS AND MOULINS
We are now immediately below the great ice-fall, and the surface
of the glacier presents an appearance not unlike the back of some
enormous caterpillar wrinkled transversely by crevasses, which close
up as we proceed downwards, and furrowed longitudinally by two
large or main watercourses whose icy banks are in places 100 feet
above their respective torrents. These two small rivers are fed from
every direction by minor watercourses, and a mile or two further
down discharge all their contents into crevasses and moulins, or
water-shafts in the ice.
GLACIER TABLES AND CONES—THE ACTION OF WARMTH
The locality of the glacier on which we now are is very interesting,
for Nature’s mills are here seen at work day by day. Glacier tables—
blocks of rock perched upon pedestals of ice formed by the
protection from the action of the sun’s warmth—are of frequent
occurrence. Glacier cones—heaps of sand and small fragments of
rock raised by a similar agency (after having been washed to one
spot by water)—are in places all around us. Then, strange and
contradictory as it may seem, we see thousands of holes, each with
a stone at the bottom and filled with the bluest of blue water,
formed also in the first place by the rays of the sun warming the
stone and causing it to sink in the ice. It is well-known in physics
that water at 39° Fahr. is at its heaviest, and as soon as the warm
stone—the dark colour of the stone having absorbed more heat than
the surrounding ice—begins to sink the warmer water follows it,
whilst that in the neighbouring temperature of 32° Fahr. rises to the
surface and becomes in its turn re-warmed, and so on. This peculiar
current often bores the holes in the ice to a depth of many feet, and
is only checked by a preponderance of cold. It is the larger stones,
therefore, which rise upon the ice, and the smaller ones which sink.
‘SURFACE’ AND ‘TERMINAL’ MORAINES
We walk on down the ice stream, and soon the moraines on either
hand close in upon us and we find ourselves on a mere wedge of
ice, at the point of which we step on to the ‘surface’ moraine. Here
the swearing begins, and it lasts right on to the terminal face four or
five miles below, for it is one continual repetition of walking on loose
and tumbling rocks, up one hillock, along a ridge, jumping from
Rock to rock with many a shock,
down another hillock, now and then starting a whole avalanche of
many-sided and sharp-edged stones down a treacherous slope of
ice, which we take for a surface deeply covered and sound of
footing.
Skate on the surface of a glacier?
‘Not much!’ (as the Colonials say).
AVALANCHES
Very strange notions also exist amongst the uninitiated as to the
nature of avalanches. The popular idea of an avalanche is derived
from heartrending accounts of great sweepings away and
annihilation of whole villages, and few of the general run of people
seem to realise that in Alpine work almost any little descending mass
of rock, snow, or ice is dignified by the name of avalanche. Snow
avalanches are most frequent after fresh falls of snow followed
immediately by warm weather, and after a little experience amongst
the mountains one soon learns to detect their customary tracks. Ice
avalanches are mainly caused through the overhanging portion of ice
at the terminals of secondary glaciers—that is, glaciers which break
off before descending to the valley or to the parent glacier below.
The tracks of ice avalanches are almost invariably unmistakable and
are swept night and day without cessation, and very frequently at
regular intervals.
Rock avalanches are more treacherous, and one never knows
when to expect them from above; generally in the early morning the
frost holds the stones above in an icy grip, but as the sun melts the
ice in the chinks the hold is released and a stone will descend into
the couloirs or ditches which scarp the mountain side. If one
happens to be below then it is a case of sauve qui peut and a rush
for the nearest protection, for there is no saying how many tons, or
indeed how many hundreds of tons, of loose rocks or stone may
start in a wild and dusty rattle down the hillside.
But some snow avalanches almost crawl down the couloirs, and
make a strange and ever-continued hissing as they move. These are
composed of heavy and sodden snow, and begin after the sun has
been up for some hours, continuing until nightfall. These are not so
dangerous on a gentle slope, and one can often waddle or half
glissade down in the midst of one with perfect safety, though they
make one uncomfortably wet.
CORNICES
Cornices are a frequent source of danger to the mountaineer. They
are formed by the snow drifting over one edge of a ridge and
forming a hanging mass. It is needless to say that one soon learns
to walk some feet away from the outer edge of a cornice, for after
poking one’s axe-handle through three feet of snow, and peeping
through a blue hole down a precipice of perhaps 1,000 feet or so, it
is not difficult to fancy what the result would be should the cornice
break.
CHAPTER XI
CANOEING ON THE NEW ZEALAND RIVERS
The Waimakariri—The enormous rainfall—Descent of
the Waitaki River—The Tasman branch—Lake
Pukaki—Leaky canoes—The Pukaki Rapids—The
Waitaki Gorge—Out on the plains again—Sixty
miles’ paddle to catch the train—Home once more
Canoeing on the New Zealand rivers is desperately exciting work. On
the west coast of the South Island there is a canoe club, whose
members build boats in watertight compartments specially suited for
the rough journeys which they undertake. Some of these men are
adepts at canoe-sailing, and think little of going out to sea in their
cockle-shells and even making long coastal journeys. The brothers
Park have established quite a reputation by their adventurous
journeyings. On one occasion they crossed the South Island with
their canoes, towing up the Teramakau River, crossing a saddle of
1,700 feet at its head, descending the Hurunui and then coasting
fifty miles down to Christchurch. On another occasion the crossing of
Cook Straits was effected by them.
On the eastern side of the island not much canoeing has been
done, with the exception of the navigation of two of the largest
rivers (the Waimakariri and Waitaki) from their sources to the sea by
Mr. Dixon and myself.
I well remember how universal was the outcry against our
attempting to descend the Waimakariri in 1889, upon which occasion
we conveyed the canoes up to the head waters in the Southern Alps,
and came down ninety miles of rapids at a tremendous rate, going
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  • 5. Computational biochemistry and biophysics 1st Edition Oren M. Becker Digital Instant Download Author(s): Oren M. Becker, Alexander D. MacKerell Jr., Benoit Roux, Masakatsu Watanabe ISBN(s): 9780824704551, 082470455X Edition: 1st File Details: PDF, 5.33 MB Year: 2001 Language: english
  • 8. ISBN: 0-8247-0455-X This book is printed on acid-free paper. Headquarters Marcel Dekker, Inc. 270 Madison Avenue, New York, NY 10016 tel: 212-696-9000; fax: 212-685-4540 Eastern Hemisphere Distribution Marcel Dekker AG Hutgasse 4, Postfach 812, CH-4001 Basel, Switzerland tel: 41-61-261-8482; fax: 41-61-261-8896 World Wide Web http://www.dekker.com The publisher offers discounts on this book when ordered in bulk quantities. For more information, write to Special Sales/Professional Marketing at the headquarters address above. Copyright  2001 by Marcel Dekker, Inc. All Rights Reserved. Neither this book nor any part may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopying, microfilming, and recording, or by any informa- tion storage and retrieval system, without permission in writing from the publisher. Current printing (last digit): 10 9 8 7 6 5 4 3 2 1 PRINTED IN THE UNITED STATES OF AMERICA
  • 9. Foreword The long-range goal of molecular approaches to biology is to describe living systems in terms of chemistry and physics. Over the last 70 years great progress has been made in applying the quantum mechanical equations representing the underlying physical laws to chemical problems involving the structures and reactions of small molecules. This work was recognized in the awarding of the Nobel Prize in Chemistry to Walter Kohn and John Pople in 1998. Computational studies of mesoscopic systems of biological interest have been attempted only more recently. Classical mechanics is adequate for describing most of the properties of these systems, and the molecular dynamics simulation method is the most important theoretical approach used in such studies. The first molecular dynamics simulation of a protein, the bovine pancreatic trypsin inhibitor (BPTI), was published more than 20 years ago [1]. Although the simulation was ‘‘crude’’ by present standards, it was important because it introduced an important conceptual change in our view of biomolecules. The classic view of biopolymers, like proteins and nucleic acids, had been static in character. The remarkable detail evident in the protein crystal structures available at that time led to an image of ‘‘rigid’’ biomolecules with every atom fixed in place [2]. The molecular dynamics simulation of BPTI was instrumental in changing the static view of the structure of biomolecules to a dynamic picture. It is now recognized that the atoms of which biopolymers are composed are in a state of constant motion at ordinary tempera- tures. The X-ray structure of a protein provides the average atomic positions, but the atoms exhibit fluidlike motions of sizable amplitudes about these averages. The new understand- ing of protein dynamics subsumed the static picture in that the average positions are still useful for the discussion of many aspects of biomolecule function in the language of structural chemistry. The recognition of the importance of fluctuations opened the way for more sophisticated and accurate interpretations of functional properties. In the intervening years, molecular dynamics simulations of biomolecules have un- dergone an explosive development and been applied to a wide range of problems [3,4]. Two attributes of molecular dynamics simulations have played an essential role in their increasing use. The first is that simulations provide individual particle motions as a func- tion of time so they can answer detailed questions about the properties of a system, often more easily than experiments. For many aspects of biomolecule function, it is these details iii
  • 10. iv Foreword that are of interest (e.g., by what pathways does oxygen get into and exit the heme pocket in myoglobin? How does the conformational change that triggers activity of ras p21 take place?). The second attribute is that, although the potential used in the simulations is approximate, it is completely under the user’s control, so that by removing or altering specific contributions to the potential, their role in determining a given property can be examined. This is most graphically demonstrated in the calculation of free energy differ- ences by ‘‘computer alchemy’’ in which the potential is transmuted reversibly from that representing one system to another during a simulation [5]. There are three types of applications of molecular dynamics simulation methods in the study of macromolecules of biological interest, as in other areas that use such simula- tions. The first uses the simulation simply as a means of sampling configuration space. This is involved in the utilization of molecular dynamics, often with simulated annealing protocols, to determine or refine structures with data obtained from experiments, such as X-ray diffraction. The second uses simulations to determine equilibrium averages, includ- ing structural and motional properties (e.g., atomic mean-square fluctuation amplitudes) and the thermodynamics of the system. For such applications, it is necessary that the simulations adequately sample configuration space, as in the first application, with the additional condition that each point be weighted by the appropriate Boltzmann factor. The third area employs simulations to examine the actual dynamics. Here not only is adequate sampling of configuration space with appropriate Boltzmann weighting required, but it must be done so as to properly represent the time development of the system. For the first two areas, Monte Carlo simulations, as well as molecular dynamics, can be utilized. By contrast, in the third area where the motions and their development are of interest, only molecular dynamics can provide the necessary information. The three types of applica- tions, all of which are considered in the present volume, make increasing demands on the simulation methodology in terms of the accuracy that is required. In the early years of molecular dynamics simulations of biomolecules, almost all scientists working in the field received specialized training (as graduate students and/or postdoctoral fellows) that provided a detailed understanding of the power and limitations of the approach. Now that the methodology is becoming more accessible (in terms of ease of application of generally distributed programs and the availability of the required computational resources) and better validated (in terms of published results), many people are beginning to use simulation technology without training in the area. Molecular dynam- ics simulations are becoming part of the ‘‘tool kit’’ used by everyone, even experimental- ists, who wish to obtain an understanding of the structure and function of biomolecules. To be able to do this effectively, a person must have access to sources from which he or she can obtain the background required for meaningful applications of the simulation methodology. This volume has an important role to play in the transition of the field from one limited to specialists (although they will continue to be needed to improve the methodology and extend its applicability) to the mainstream of molecular biology. The emphasis on an in-depth description of the computational methodology will make the volume useful as an introduction to the field for many people who are doing simulations for the first time. They will find it helpful also to look at two earlier volumes on macro- molecular simulations [3,4], as well as the classic general text on molecular dynamics [6]. Equally important in the volume is the connection made with X-ray, neutron scatter- ing, and nuclear magnetic resonance experiments, areas in which molecular dynamics simulations are playing an essential role. A number of well-chosen ‘‘special topics’’ in- volving applications of simulation methods are described. Also, several chapters broaden
  • 11. Foreword v the perspective of the book by introducing approaches other than molecular dynamics for modeling proteins and their interactions. They make the connection with what many peo- ple regard—mistakenly, in my view—as ‘‘computational biology.’’ Certainly with the announced completion of a description of the human genome in a coarse-grained sense, the part of computational biology concerned with the prediction of the structure and func- tion of gene products from a knowledge of the polypeptide sequence is an important endeavor. However, equally important, and probably more so in the long run, is the bio- physical aspect of computational biology. The first set of Investigators in Computational Biology chosen this year demonstrates that the Howard Hughes Foundation recognized the importance of such biophysical studies to which this volume serves as an excellent introduction. I am very pleased to have been given the opportunity to contribute a Foreword to this very useful book. It is a particular pleasure for me to do so because all the editors and fifteen of the authors are alumni of my research group at Harvard, where molecular dynamics simulations of biomolecules originated. REFERENCES 1. JA McCammon, BR Gelin, and M Karplus. Nature 267:585, 1977. 2. DC Phillips. In: RH Sarma, ed. Biomolecular Stereodynamics, II. Guilderland, New York: Ade- nine Press, 1981, p 497. 3. JA McCammon and S Harvey. Dynamics of Proteins and Nucleic Acids. Cambridge: Cambridge University Press, 1987. 4. CL Brooks III, M Karplus, and BM Pettitt. Proteins: A Theoretical Perspective of Dynamics, Structure, and Thermodynamics. New York: John Wiley & Sons, 1988. 5. For an early example, see J Gao, K Kuczera, B Tidor, and M Karplus. Science 244:1069–1072, 1989. 6. MP Allen and DJ Tildesley. Computer Simulations of Liquids. Oxford: Clarendon Press, 1987. Martin Karplus Laboratoire de chimie Biophysique, ISIS Université Louis Pasteur Strasbourg, France and Department of Chemistry and Chemical Biology Harvard University Cambridge, Massachusetts
  • 13. Preface The first dynamical simulation of a protein based on a detailed atomic model was reported in 1977. Since then, the uses of various theoretical and computational approaches have contributed tremendously to our understanding of complex biomolecular systems such as proteins, nucleic acids, and bilayer membranes. By providing detailed information on biomolecular systems that is often experimentally inaccessible, computational approaches based on detailed atomic models can help in the current efforts to understand the relation- ship of the structure of biomolecules to their function. For that reason, they are now considered to be an integrated and essential component of research in modern biology, biochemistry, and biophysics. A number of books and journal articles reviewing computational methods relevant to biophysical problems have been published in the last decade. Two of the most popular texts, however, were published more than ten years ago: those of McCammon and Harvey in 1987 and Brooks, Karplus, and Pettitt in 1988. There has been significant progress in theoretical and computational methodologies since the publication of these books. There- fore, we feel that there is a need for an updated, comprehensive text including the most recent developments and applications in the field. In recent years the significant increase in computer power along with the implemen- tation of a wide range of theoretical methods into sophisticated simulation programs have greatly expanded the applicability of computational approaches to biological systems. The expansion is such that interesting applications to important and complex biomolecular systems are now often carried out by researchers with no special training in computational methodologies. To successfully apply computational approaches to their systems of inter- est, these ‘‘nonspecialists’’ must make several important choices about the proper methods and techniques for the particular question that they are trying to address. We believe that a good understanding of the theory behind the myriad of computational methods and techniques can help in this process. Therefore, one of this book’s aims is to provide readers with the required background to properly design and implement computational investiga- tions of biomolecular systems. In addition, the book provides the needed information for calculating and interpreting experimentally observed properties on the basis of the results generated by computer simulations. vii
  • 14. viii Preface This book is organized so that nonspecialists as well as more advanced users can benefit. It can serve as both an introductory text to computational biology, making it useful for students, and a reference source for active researchers in the field. We have tried to compile a comprehensive but reasonably concise review of relevant theoretical and computational methods that is self-contained. Therefore, the chapters, particularly in Part I, are ordered so that the reader can easily follow from one topic to the next and be systematically introduced to the theoretical methods used in computational studies of bio- molecular systems. The remainder of the book is designed so that the individual parts as well as their chapters can be read independently. Additional technical details can be found in the references listed in each chapter. Thus the book may also serve as a useful reference for both theoreticians and experimentalists in all areas of biophysics and biochemical research. This volume thus presents a current and comprehensive account of computational methods and their application to biological macromolecules. We hope that it will serve as a useful tool to guide future investigations of proteins, nucleic acids, and biological membranes, so that the mysteries of biological molecules can continue to be revealed. We are grateful to the many colleagues we have worked with, collaborated with, and grown with over the course of our research careers. The multidimensionality of those interactions has allowed us to grow in many facets of our lives. Special thanks to Professor Martin Karplus for contributing the Foreword of this book and, most important, for supply- ing the insights, knowledge, and environment that laid the foundation for our scientific pursuits in computational biochemistry and biophysics and led directly to the creation of this book. Finally, we wish to acknowledge the support of all our friends and family. Oren M. Becker Alexander D. MacKerell, Jr. Benoı̂t Roux Masakatsu Watanabe
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  • 16. Harper and myself, and soon we had the tent pitched and were snug for the night. At three o’clock on the Saturday morning Dixon and I crawled out of our sleeping-bags, and by 4 a.m. we were on the snow slopes, determined to make a vigorous attack upon the peak which had so long defied us. Two hours on fairly good snow slopes and a scramble over a nasty slab-like face of rock, and once again the plateau, and that glorious scene of Aorangi and Tasman, were before us. But the wind had risen quickly and was blowing a gale from the south-west—the cold quarter. To face such a wind for any length of time, or to attempt to climb Aorangi against it, would be simple madness, so we turned and ignominiously fled to the refuge of our bivouac, 1,200 feet below, which we reached at seven o’clock, having been but three hours absent. We then sent Annan down, as we were keeping him from his work in the lower country, telling him to leave word with the survey party that if we did not arrive back at the Ball Glacier by Monday night something would probably have gone amiss with us. During the day the gale blew itself out, and next morning at 3.45 we were in our steps of the day before, reaching the plateau in an hour and a half. The morning sun lit up the peaks with a rosy glow, soon his piercing beams forced us to put on the goggles, while the crust of the snow began to soften under the great power of penetration which the rays possess in the rarefied air. This forced us to plod onward in slushy snow as we headed right for the Linda Glacier, which we could see rounding the point of the north-eastern arête of our mountain. On our right rose Mount Tasman clothed in ice, from which during the night an immense avalanche had descended. We walked close to its furthest point of motion as it lay stretched out on the level snow- field like a gigantic breakwater, and found it to be 300 paces in width; Dixon estimated that it covered from forty to fifty acres.
  • 17. We now put on the rope, as crevasses began to appear in the gently rising slopes to the Linda Glacier. On our left we thought that the north-eastern ridge looked practicable, but deemed it better to rely on a route chosen by so able a mountaineer as Ulrich Kaufmann, and kept on our course for the Linda Glacier, taking ten- minute spells at leading and breaking steps in the soft and slushy snow, and winding our way amongst ever-increasing crevasses in search of snow bridges over which we would cautiously crawl. Now we would have a stretch of gently rising snow, then a crevasse or perhaps a bergschrund, followed by a steep ascent for 100 or 200 feet, then a divergence to one side or the other to avoid a chaos of séracs or blocks of tumbled and broken ice; and so on, hour after hour. About noon we had gained a considerable elevation above the plateau and were well round the corner on the Linda Glacier. Into this elevated valley the sun poured down through a rarefied atmosphere on to slopes on either hand which reflected all the light and heat. The glare was something dreadful, and before midday our faces and hands had assumed the customary chocolate colour, and the skin was literally broiled off me; Dixon did not suffer to such an extent. The heat was most intense, though not of the enervating kind which one feels at lower altitudes. Viewed from this quarter Aorangi presents a totally different form than from any other, and we began to be sanguine about accomplishing our task. I was in possession of notes and sketches of the route kindly sent me by Mr. Green, and these were of material assistance to us. Before us lay the final peak with its capping of ice. From the summit, now in full view, descended in a north-westerly direction to the right a steep rocky arête connecting with the ridge leading on to Mount Tasman. From the lower parts of these rocks steep ice slopes streaked with marks from falling rocks descend to the upper portions of the Linda Glacier, bounded all along their lower termination by an immense bergschrund which severs them from immediate contact with the glacier itself.
  • 18. On the left of the summit slopes the north-eastern arête, consisting of a ridge of alternate knife-edges of ice and gensdarmes or towers of rock. The northern side or face of this ridge descending to the Linda Glacier is composed of very steep slopes of ice set with three immense masses of red sandstone rocks, with two ice-filled couloirs or ditches between them. Up these two couloirs lay our route. We thought, however, that by leaving the glacier and taking to the crest of the ridge we could improve on the route, but soon found that the change was a mistake, and so struck back on to our old course up the middle of the glacier, the final slopes of which were very steep and exposed to the chance of avalanches from either hand. It seemed a hopeless task this plunging through soft snow hour after hour, and it was nearly one o’clock ere we gained the edge of the big bergschrund and with difficulty discovered a sound enough snow bridge. Shortly before this an incident occurred in crossing one of these snow bridges which brought forcibly before our minds the serious nature of the work in which we were engaged. I—the lighter man by two stone—had crawled over in safety, and planting myself well in the soft snow above, was taking in the slack of the rope as Dixon followed, when suddenly he went through up to his armpits and was dangling in space, held up by a thin crust of snow and by the rope from above. I pulled with the strength of despair, and Dixon struggled till he secured a hold somehow on the other lip of the crevasse and got out. That sort of thing is all very well to look back upon and talk over afterwards, but I am not likely to forget for many a long day the sensation of holding up a thirteen-stone man under such circumstances, and I must say that I should have been much easier in my mind if we had had such a man as Emil Boss or Ulrich Kaufmann on one end of the rope. Immediately after crossing the big bergschrund step-cutting commenced; and from this point upwards every step, other than those on rocks, had to be cut in hard ice.
  • 19. It is no easy task after climbing steadily for nine hours in soft snow to set to work and cut steps, especially when one knows that a slip must on no account be made, for with two men only on the rope it would mean a sudden descent to the crevasses or precipices (as the case may be) below, and our certain destruction. An hour’s steady work and we gained the foot of the lowest rocks, which were found to be quite unscalable. We then sidled round the base of these rocks to the left and commenced cutting steps up the first couloir, keeping close into the rocks on our right, on which we could get an occasional hand-grip. Ice blocks were continually coming down from the broken masses overhanging the top of the couloir, but luckily none struck us. The descent of an ice block in such steep ice slopes is something to remember. First a rattle above, and then ‘swish, swish’ as the first leaps begin, followed by a ‘whir-r- r-r’ and a ‘hum-m-m-m’ as, like a flash of light, a spinning and ricochetting object goes by and is lost to sight over the brink of the precipice below, or perchance is detected spending its momentum on the soft snow slopes 1,000 feet down. These falls of ice on the upper slopes are not like the hissing avalanches, which sometimes even crawl down the lower snow slopes, but come down with the speed of light, and are calculated to strike terror into the heart of the stoutest-nerved climber. We crossed the couloir near its head, partly on ice and partly on rocks, amid the gravest peril from showers of ice, and took to the rocks on our left, which were both dangerous and difficult, mainly owing to their being here and there coated with ice. Soon they became quite inaccessible, and we were again forced towards our left on to the ice slopes in the second couloir, and here we found the ice even harder, and we could only make an impression on it with the spike end of our axes. To add to the difficulty, the angle of ascent became steeper, inclining in places to about 60° from the horizontal. We negotiated this couloir in a similar manner to that below, but water trickling from the overhanging rocks formed awkward
  • 20. hummocks of ice on the slope close to the rocks, over which we thought it almost impossible to climb, and to go out into the middle of the couloir was impossible, owing to falling ice. Time was quickly passing, and we had a terrible fight to reach the head of the couloir. The rocks now shaded us from the sun’s rays, and soon our hats, coats, and the rope were frozen as stiff as boards, while the cold was so intense as to cause the skin of our hands to adhere to the steel of the ice-axes. It seemed now more than ever a hopeless task to reach the final ice-cap, which we knew could not be far above us; but we silently and doggedly cut away, and at length were rewarded by finding the rocks on our right practicable; taking to them we were soon on their crest, and the ice-cap of the mountain lay straight before us. An easy bit of rock-climbing led up to the slopes, which we found to be covered with a peculiar form of lumpy and frozen drifted snow. At the top of the rocks we looked around in vain for Mr. Green’s cairn, with his handkerchief and Kaufmann’s matchbox, left on the occasion of their ascent in March 1882. Doubtless they have either been long since swept away by falling ice or were buried in the terminal of the ice slope, which in December would encroach farther down upon the rocks than in March. Dixon now counselled a retreat, arguing that we had virtually overcome all the difficulties and had only the final and easy slope to cut up; but I persuaded him to stay a little longer and make a push for it, or at least as much of a push as we were capable of making.
  • 21. AORANGI: THE HIGHEST PEAK [From a Water-colour Sketch It was half-past five. Four hours and a half we had been toiling from the head of the Linda Glacier, thirteen hours and a half from our bivouac, without any halt to speak of. A wind began to blow from the north-west, adding fresh cause for anxiety about the descent. One thing was certain—if we wanted to get down alive we should have to reach the Linda Glacier again before dark. We worked as hard as we were able at step-cutting for another fifteen minutes, but only made slow progress; yet there was the cornice, just away to the right, the crest of the ridge to the left, and the top scarcely a stone’s throw above, with no difficulty in the way. What would we not have given for another hour of daylight? How could we turn away when so near to a complete victory over our old foe?
  • 22. Dixon again suggested turning, and I could not do otherwise than defer to his advice, for already we were caught in a trap, and should bad weather come upon us—and the wind and cold were fast increasing—before we reached the Linda Glacier again the probabilities were that we never should have returned from the giddy heights of the great Aorangi, the ‘Sky-piercer.’ The height of the mountain is 12,349 feet; our aneroid read at our turning-point 12,300, and we reckoned the summit to be 140 feet above us. The slight error in the reading of the instrument would be accounted for by the impending change of weather. The view is magnificently comprehensive. Looking northwards we could see clear over the top of our giant neighbour, Mount Tasman (11,475 feet). On the western side, the ocean, but twenty miles distant, was covered by a mantle of low-lying clouds creeping into the bays and inlets of the coast, studded here and there with islanded hill-tops, and stretching away to what seemed a limitless horizon on the west. A streak of blue ocean showed through the cloud mantle near Hokitika, seventy miles northwards. North-eastwards the glorious array of the Southern Alps extended, presenting a panorama of such magnificence and comprehensiveness that it defies any attempt at description. It is one of those vast pictures which are indelibly impressed upon the memory—one of those overpowering examples of Nature’s sublimity which seem to move a man’s very soul and call him to a sense of his own littleness. Close under us lay the scenes of all our joys and sorrows of the past five years: the Tasman Glacier, encircled by those splendid peaks and snow-fields whose forms we had learned to know and love so well; further afield lay the Liebig Range, and, showing over this, Mount Jukes and his attendant satellites of rocky peaks. Beyond this again, far, far away in the blue and indefinite east, we could distinguish the hills of Banks Peninsula, close to our homes near Christchurch, whilst we could imagine that the blue haze
  • 23. distinguishable there was indeed the eastern ocean, 120 miles distant. It will, of course, be said that we did not make the complete ascent of the mountain. Be that so; neither does Mr. Green claim that honour, though for all practical purposes to be on the ice-cap of Aorangi means the same thing as being on the top. Mr. Green’s highest point must, according to his sketches, have been as nearly as possible 100 feet above ours. But we could not spare time to moralise and rest as we should like to have done, for it was imperative that the terrible ice slopes should be descended before the light failed, and at a few minutes to six we began to go down backwards in our steps, taking a firm hold with our axes at every step. This going down is a fearful strain on the nerves, and requires the greatest steadiness and caution. In hurrying down the easy rocks we missed a mark on a snow patch which Dixon had made to denote the right route, and this mistake at the outset caused us nearly half an hour’s delay before we found the right spot from which to leave the crest of the rocks. Dixon led down the rocks and I followed, every now and then taking a turn round any prominent projection with the rope and easing him down, whilst he in turn secured a good hold and took in the slack as I came down. Bad as it had been coming up the top couloir, it was infinitely worse going down, for what was trickling water on the upward journey was now solid ice, and many of the steps were filled with re- frozen chips of ice from the steps we had cut above, and these had to be cleaned out before we could get a secure foothold. Cutting steps up is one thing, and cutting them down another, for on a steep slope one cannot turn round face downwards to get at one’s work, which in the case of going up-hill lies convenient to the hand. How we did get down without the fatal slip which I was momentarily expecting would be made by one or the other of us I
  • 24. never could quite understand. The rocks below the topmost couloir were negotiated and the lower couloir reached. This was not so difficult to descend, and the effect of the frost was such as to prevent such a continual shower of ice blocks from above, thus minimising one prominent danger. The lower parts of the couloir were reached, and here are situated the rocks which form the ledge upon which with Boss and Kaufmann Mr. Green stood out for the night. There are several ledges accessible, but Mr. Green’s party must have been upon one of the higher, for on some of the lower ledges there is room for a dozen men to stand or even lie down, though scarcely space enough for a circus or Wild West show, as Dixon humorously suggested. The light was now fast failing, and we strained every nerve to reach the big bergschrund below before darkness was upon us. We were just in time and that was all, and the frail snow bridge was passed by our sliding over on our backs; I, the lighter man, led, and Dixon followed as steady as a rock—not a Mount Cook Rock, but the proverbial one. We had now been seventeen hours with every nerve and muscle constantly in action, and yet, as the darkness set in and the awful glare of the sun had left us, we began to freshen up, and lighting one of our Austrian climbing-lanterns we retraced our footsteps of the morning, being most careful never to deviate from them. Soon it became very dark, for there was no moon, and we could but dimly distinguish the ghostly forms of the white-robed peaks which shut us in on all hands. Hour after hour we plodded on. On one occasion we were brought up by the crevasse into which Dixon had nearly fallen in the morning; it had opened wider during the day, and only after walking along its line of fracture in both directions for half an hour did we discover a bridge which seemed sufficiently strong. We crossed in our usual way, sliding over at full length, and putting some weight
  • 25. on to our axe-handles laid lengthways on the snow to distribute the weight as much as possible. As the night wore on, the crust of the snow became harder, and after passing through that most unpleasant crusted stage when it will bear until all the weight is put on one foot, became quite pleasant to walk upon, and over the lower part of the Linda Glacier and across the plateau we made a fair pace. As we reached the rise off the plateau on to the Haast Ridge the wind increased in violence, and we had great difficulty in keeping our lanterns (two of which we now kept going) alight. The crest of the ridge was gained, and the descent of the dangerous snow slopes to the bivouac, 1,200 or 1,400 feet below, commenced. We were soon in trouble again amongst bergschrunds and crevasses, and on two occasions, in going down and feeling for the next step behind, I found on showing a light that my hind leg was dangling in a crevasse! I must not weary you, dear reader, with further monotonous descriptions of crossing these deadly enemies of the mountaineer, suffice it to say that after an exasperating hunt on the steep slopes and in the dark for our bivouac—the candles being just finished—we finally discovered it at 2.45 a.m., an hour before daylight, having been twenty-three hours constantly hard at work without any halt worthy the name. Sleeping soundly till 9 a.m. we made up our swags, and by 11 a.m. were on the downward route again for the Ball Glacier camp. It was quite a wrench to leave our friendly rock, which had become a haven of rest and refuge to us on this upper beat. Five nights have I spent under its protection at different times, and as often have I arisen with the early morn to gaze upon those vast and sublime solitudes of Nature so grandly unfolded to view. From this little home—out of which if one stepped one had to be careful not to lose one’s footing and make a rapid descent to the Hochstetter Glacier on one hand or to the Freshfield on the other—I have seen
  • 26. the rosy tints of the newly-born day creep downwards from the hoary snow-caps of the mountains, and when evening drew on have watched the afterglow envelop all in its warm embrace, even black rocks turning to a deep crimson which seemed to pervade the higher peaks ere the black and cold night once again grasps them in his icy hold. Here had tired limbs been laid to rest whilst wearied minds dreamed dreams of success and hope, gaining renewed vigour with the morning light to go forth afresh into new struggles and enjoyments. Here in the heart of great Nature’s solitudes the thoughts flew back to homes of comfort and of love. What wonder that we should have formed associations with such a spot? The Ball Glacier camp was reached at 4.30 p.m., where we found Mr. Sladden of the Survey party anxiously awaiting our arrival, with that forethought which shows the kindly feeling and consideration for others that characterises men of worth in these outlandish parts. That evening Dixon went across with Sladden to the Survey camp in the Murchison Valley, leaving me to wait for an expected friend from Christchurch. Here I was quite alone amongst the mountains, with plenty of time to muse over the events of the past few days and to let my wandering thoughts fly back even further, to the struggles of the past five years whilst attempting to conquer Aorangi. What is the climber’s reward for all his trouble? Why does he climb? Who can tell? Is it renown he struggles for? No; I am convinced that is a very infinitesimal motive. For mercenary ends? No; there is no financial harvest to reap. I have often tried to think why men undergo such labour and hardship, but cannot come to any definite conclusion. To overcome set tasks (‘pure cussedness’ the Americans would say) is one reason (after once putting one’s hand to the plough). To gain physical and mental strength, to raise and purify the mind in Nature’s great
  • 27. school, are both potent reasons. But, above all, there is some mysterious influence pervading all true mountaineers—a mountain fever, a close kinship with Nature (call it what you will), a hidden impulse that grows on a man who has once felt what it is to taste the sweets of climbing and to enjoy the fascinations of the world above the snow-line. My friend did not arrive, so I made my way over to Mr. Brodrick’s Survey camp on the Murchison, walking through a thick mist, and steering across the Tasman by the aid of a compass—a distance of seven miles, or three hours’ walking from camp to camp. Here I found Cooper—Messrs. Wheeler & Son’s photographic operator—who was down securing views of the district for a lecture which I was to deliver before the Australasian Association for the Advancement of Science. It was our intention to make a two days’ excursion up the Murchison Glacier with Cooper, but showery weather put a veto on our plans, and we were fain to be content with a short excursion to the Onslow Glacier, where some exposures were effected. Leaving Mr. Brodrick’s hospitable quarters on December 10, by the 12th we were again at the Hermitage.
  • 29. CHAPTER X ON SOME OF THE PHENOMENA OF GLACIERS, WITH SPECIAL REGARD TO THOSE OF NEW ZEALAND The cause of glaciers—Formation and structure— Motion—Moraines: Lateral, medial, and terminal —‘Surface’ moraines—Crevasses—Moulins—Glacier cones—Glacier tables—Surface torrents— Avalanches—Cornices In a work of this nature it may not be out of place to briefly describe some of those interesting features and phenomena which accompany the world above the snow-line. Here is a quotation from a recent review of Professor Heim’s work[2] by a prominent member of the English Alpine Club:— ‘Some thirty years ago a systematic résumé of all that was known up to that date about existing glaciers appeared in the work of Professor Albert Mousson, “Die Gletscher der Jetztzeit,” since which, with perhaps the exception of Major Hüber’s “Les Glaciers,” no attempt has been made to collect into a focus the light which numerous able observers and theorists have subsequently thrown upon the question. The intricacy of the problem has, indeed, increased almost in proportion to our enlarged knowledge of its conditions; and in spite of the labours of a large and very
  • 30. distinguished body of investigators, not only do many important points remain matters of dispute, but the very materials for a complete solution are still wanting.’ [2] Handbuch der Gletscherkunde, von Dr. Albert Heim, Zürich (Stuttgart: Verlag von J. Engelhorn, 1885, 18 francs.) CAUSE OF GLACIERS The joint cause of glaciers is precipitation and cold. A low temperature alone can do nothing without moisture, and this fact quickly disposes of the popular notion that glaciers invariably exist in cold countries. Thibet, for instance, and also some parts of Arctic North America are destitute of ice streams, though eternal cold may be said to reign supreme in these parts. Imagine for a moment the higher mountains clear of snow and ice, and then watch for the formation of a glacier. Snow falls and fills up all the valleys and gullies, avalanches descend from the higher parts, and a great accumulation gathers in all hollows. By constant repetition of snow-falls (always provided a greater quantity is deposited than can be melted by the sun’s rays and by the natural warmth of the earth’s crust) great pressure is put upon the lower portions by the superincumbent accumulation, and aided by the infiltration of water and refreezing (or ‘regelation’ as the correct term is), a large body of ice is formed which at once begins to move down the valleys containing it. GLACIER ICE Glacier ice is not like the solid blue ice on the surface of water, but consists of granules joined together by an intricate network of capillary water-filled fissures. In exposed sections and upon the surface of the ice can be observed a ‘veined’ or ‘banded’ structure—veins of a denser blue
  • 31. colour alternating with those of a lighter shade containing air bubbles. The cause of this peculiar structure has been the subject of much theorising amongst investigators, but hitherto I believe the greatest authorities consider that the explanation of the phenomenon is yet wanting. GLACIER MOTION The motion of glaciers is yet another bone of contention, but it is generally admitted that the cause of it is to be found mainly in gravitation, and is also partially accounted for by the strange property of ‘viscosity’ in what appears to the casual observer to be nothing more or less than a rigid solid. Recently observations for ascertaining the rate of progress of the Tasman, Murchison, Hooker, and Mueller Glaciers have been made by the New Zealand Government Survey Department. Some of the results were embodied in a paper by Mr. J. H. Baker, the Chief Surveyor of the Provincial District of Canterbury, and will appear in the ‘Transactions of the Australasian Association for the Advancement of Science’ for 1891. At the late meeting of that body a committee was appointed to further these investigations, and a sum of 25l. voted for the aid of the same. Before long, therefore, there will be put before the scientific public reliable measurements of the motion of several of the largest and least-known glaciers in temperate regions. MORAINES There is a remarkable feature of the glaciers of this country which stamps them as unique in one respect—I refer to the very extensive moraines. I write feelingly of this, for my acquaintance with them has been a very close one, and they have impressed me very deeply —in more ways than one.
  • 32. The large glaciers of which I have written in this work are completely moraine-covered over their lower parts. ‘SURFACE’ MORAINES Moraines may be divided into four sections: ‘Lateral’ moraines, fringing the sides of the glaciers, their outlying portions often being ‘dead’—that is, at present unmoved by the action of the ice, and forming banks, as it were, for the ice stream to flow between; ‘medial’ moraines, which begin at the junction of two streams of ice and often continue for many miles to the terminal face; ‘terminal’ moraines, formed by the depositing of detritus at the melting point or end of the glacier; and, lastly, ‘surface’ moraines (so called by Professor Hutton of Christchurch, N.Z.), which are the combined accumulations of the first two divisions in the lower parts of the glacier. It is these ‘surface’ moraines that are such a characteristic feature of the glaciers situate on the eastern side of the chain in New Zealand. Of those on the western side I am not able to speak with authority, never having visited them myself; but I understand that they do not carry such a large quantity of detritus as those of the eastern slopes. This disparity remains to be accounted for and awaits an explanation. I have a theory of my own upon the subject, which, however, as yet I would not like to put too strongly forward. On both sides of Mount Cook, on Mount De la Bêche (ten miles further along the chain), and on a peak just north of the Hochstetter Dome (ten miles still further north) I have observed enormous exposed sections of the rock strata, which in each case dip at a steep angle from east to west, presenting slab faces, not easily disturbed by the action of the frost, to the westward, but broken and fast denuding faces (‘basset’ faces, as they are geologically termed) to the eastward. I am hoping at some future time to further investigate this interesting subject.
  • 33. As the western glaciers, however, must descend steeper valleys than the eastern, I make no doubt that their rate of progress will be eventually ascertained to be greater than that of the latter, and this would militate largely against an accumulation of moraine upon the ice. THE SURFACE OF A GLACIER All sorts of queer notions as to what the surface of a glacier is like exist. Indeed I have often heard people inquire if it would be possible to skate upon it! Let us for a moment imagine ourselves at the head of the great Tasman Glacier, 8,600 feet above sea-level. All around us is snow, either freshly fallen or merging into névé. We begin to walk down, and at first, upon the steeper slopes, cross a few large crevasses and bergschrunds by means of snow bridges; then, as the incline becomes less steep, we walk for six miles or so upon a smooth surface of névé, or perchance knee-deep in fresh snow, and scarcely a crevasse exists. At the beginning of the great turn we gradually leave the névé and find ourselves upon hard, white ice, and soon transverse crevasses appear; these are a little further on cut by longitudinal crevasses forming the surface into huge squares, not flat on the top, but hummocky. A perfect network of crevasses cuts up the whole of the surface, but those parts on the outside of the curve are infinitely more disturbed than those on the inside, owing to the tension put upon them by the faster rate at which they have to move. After rounding the turn the glacier again consolidates and few crevasses appear, only the surface is covered with old wounds—if I may coin such a term—from the rents which have occurred at the turn, and presents a very undulating appearance. The little gullies are formed into watercourses and intersect the glacier in all directions. On our right, now, is the medial moraine formed by detritus from Mount De la Bêche, brought down partly by the Tasman and partly by the Rudolf Glaciers, and it stands up 100 feet or so above the surface of the clear ice on either side of it, owing to
  • 34. the protection from the sun’s rays afforded by it to the ice beneath, so preventing ‘ablation’ or waste going on so quickly. We follow down for another four or five miles, and then cross this moraine (which has in the meantime joined that on the northern side of the Hochstetter Glacier) on to the Hochstetter on our right. SURFACE TORRENTS AND MOULINS We are now immediately below the great ice-fall, and the surface of the glacier presents an appearance not unlike the back of some enormous caterpillar wrinkled transversely by crevasses, which close up as we proceed downwards, and furrowed longitudinally by two large or main watercourses whose icy banks are in places 100 feet above their respective torrents. These two small rivers are fed from every direction by minor watercourses, and a mile or two further down discharge all their contents into crevasses and moulins, or water-shafts in the ice. GLACIER TABLES AND CONES—THE ACTION OF WARMTH The locality of the glacier on which we now are is very interesting, for Nature’s mills are here seen at work day by day. Glacier tables— blocks of rock perched upon pedestals of ice formed by the protection from the action of the sun’s warmth—are of frequent occurrence. Glacier cones—heaps of sand and small fragments of rock raised by a similar agency (after having been washed to one spot by water)—are in places all around us. Then, strange and contradictory as it may seem, we see thousands of holes, each with a stone at the bottom and filled with the bluest of blue water, formed also in the first place by the rays of the sun warming the stone and causing it to sink in the ice. It is well-known in physics that water at 39° Fahr. is at its heaviest, and as soon as the warm stone—the dark colour of the stone having absorbed more heat than the surrounding ice—begins to sink the warmer water follows it, whilst that in the neighbouring temperature of 32° Fahr. rises to the
  • 35. surface and becomes in its turn re-warmed, and so on. This peculiar current often bores the holes in the ice to a depth of many feet, and is only checked by a preponderance of cold. It is the larger stones, therefore, which rise upon the ice, and the smaller ones which sink. ‘SURFACE’ AND ‘TERMINAL’ MORAINES We walk on down the ice stream, and soon the moraines on either hand close in upon us and we find ourselves on a mere wedge of ice, at the point of which we step on to the ‘surface’ moraine. Here the swearing begins, and it lasts right on to the terminal face four or five miles below, for it is one continual repetition of walking on loose and tumbling rocks, up one hillock, along a ridge, jumping from Rock to rock with many a shock, down another hillock, now and then starting a whole avalanche of many-sided and sharp-edged stones down a treacherous slope of ice, which we take for a surface deeply covered and sound of footing. Skate on the surface of a glacier? ‘Not much!’ (as the Colonials say). AVALANCHES Very strange notions also exist amongst the uninitiated as to the nature of avalanches. The popular idea of an avalanche is derived from heartrending accounts of great sweepings away and annihilation of whole villages, and few of the general run of people seem to realise that in Alpine work almost any little descending mass of rock, snow, or ice is dignified by the name of avalanche. Snow avalanches are most frequent after fresh falls of snow followed immediately by warm weather, and after a little experience amongst the mountains one soon learns to detect their customary tracks. Ice avalanches are mainly caused through the overhanging portion of ice at the terminals of secondary glaciers—that is, glaciers which break
  • 36. off before descending to the valley or to the parent glacier below. The tracks of ice avalanches are almost invariably unmistakable and are swept night and day without cessation, and very frequently at regular intervals. Rock avalanches are more treacherous, and one never knows when to expect them from above; generally in the early morning the frost holds the stones above in an icy grip, but as the sun melts the ice in the chinks the hold is released and a stone will descend into the couloirs or ditches which scarp the mountain side. If one happens to be below then it is a case of sauve qui peut and a rush for the nearest protection, for there is no saying how many tons, or indeed how many hundreds of tons, of loose rocks or stone may start in a wild and dusty rattle down the hillside. But some snow avalanches almost crawl down the couloirs, and make a strange and ever-continued hissing as they move. These are composed of heavy and sodden snow, and begin after the sun has been up for some hours, continuing until nightfall. These are not so dangerous on a gentle slope, and one can often waddle or half glissade down in the midst of one with perfect safety, though they make one uncomfortably wet. CORNICES Cornices are a frequent source of danger to the mountaineer. They are formed by the snow drifting over one edge of a ridge and forming a hanging mass. It is needless to say that one soon learns to walk some feet away from the outer edge of a cornice, for after poking one’s axe-handle through three feet of snow, and peeping through a blue hole down a precipice of perhaps 1,000 feet or so, it is not difficult to fancy what the result would be should the cornice break.
  • 37. CHAPTER XI CANOEING ON THE NEW ZEALAND RIVERS The Waimakariri—The enormous rainfall—Descent of the Waitaki River—The Tasman branch—Lake Pukaki—Leaky canoes—The Pukaki Rapids—The Waitaki Gorge—Out on the plains again—Sixty miles’ paddle to catch the train—Home once more Canoeing on the New Zealand rivers is desperately exciting work. On the west coast of the South Island there is a canoe club, whose members build boats in watertight compartments specially suited for the rough journeys which they undertake. Some of these men are adepts at canoe-sailing, and think little of going out to sea in their cockle-shells and even making long coastal journeys. The brothers Park have established quite a reputation by their adventurous journeyings. On one occasion they crossed the South Island with their canoes, towing up the Teramakau River, crossing a saddle of 1,700 feet at its head, descending the Hurunui and then coasting fifty miles down to Christchurch. On another occasion the crossing of Cook Straits was effected by them. On the eastern side of the island not much canoeing has been done, with the exception of the navigation of two of the largest rivers (the Waimakariri and Waitaki) from their sources to the sea by Mr. Dixon and myself. I well remember how universal was the outcry against our attempting to descend the Waimakariri in 1889, upon which occasion we conveyed the canoes up to the head waters in the Southern Alps, and came down ninety miles of rapids at a tremendous rate, going
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