OK let me tell you a little bit
about what I'm doing mostly and

working with thing in a D.N.A.
molecule within a porting complexes and

I'm very much interested in the role
that mechanics place on the second super

molecular scale in these systems
before I get into the details of it.

Let me tell you a little bit about
where some of the challenges

that bio physics and how what I'm
doing actually fits into that and

twice with of some of
the With challenge just let

me start out with what I see as one of
the biggest challenges fight now is

we need to empower physics we need to
really integrate biochemical physical and

biological description of
biological systems that I mean if

you looked at bio physics to talk
paper and bio physics that say.

Twenty years ago you could fairly
easily tell this is a physicist looking

at a biological problem or this is a
biochemist using a physical technique and

that's no longer to today.

So we need to come to an integrated
descriptions that's very much with

a few just going with that.

I mean again it's a fairly
complex structure here.

And you can take each individual P.C. and
come up often with a partial description

of it be it bio chemical bio
chemistry bio chemical pathways

structural descriptions almost
mechanical descriptions for

pump like this you can go to
the tools that some of the tools that

we have out of physics and mathematics
come up with a complex set of equations to

describe them again you know he
just one hears of photosynthesis.

You can do is quantum mechanics here too
is that we are very familiar with and

physics and
describe each little bit in piece in here.

However they are all very very tight
usually very tightly coupled together they

are really put into this very
complex system and you're not.

Physically close but also very
closely coupled in their function.

So one of the challenges really is come
up with comprehensive descriptions that

incorporate chemical physical
biological aspects of all of this.

To Will it just quite adequately
a bio logical system and

now everything so
closely together they are.

There's another difficulty here.

And that.

We have vastly different length and
time scales that we're looking at and

all of them again very tightly
coupled to each other so

time scales everything to seconds for

energy transport policies they can put a
thing to down talk lifetime of organisms.

Days at least not so even if you talk
about length scale it's just picked

my favorite example of course in
a young you have the atomistic

description we know where every atom is
in the double helix of us and Watson and

Crick then we go to a larger next larger

scale here in a wrapped around
New Kids on because arms then

organized into fibers fibers
organized into a coma zones and.

The point here is these things skids are
very tightly coupled so what's happening

here on the molecular scale effects easily
what's happening up here on the lab scale.

So for instance you know a gene is coding
for a port in that puts the commas or

minutes by change it compacts and so on so

quoting here atoms basically coding for
Eventually the shape of this year and

vice versa the overall macroscopic
structure here can affect.

Actually accessible for twenty year.

You need to know what's going.

On the commas almost scale to know

which actually base to see which could
see which atoms actually do matter and

vice versa the atoms you're caught
in the end for how this year.

Looks like how it works.

So we have a very tight coupling.

Unlike in physics they
can do just fine that

of physics without knowing much
about the elementary particles.

We have the separation
of playing scales but

physical problems usually you cannot do
that you need to come up with these mighty

scale descriptions another one a popular
example for this year we can advance that.

Double forces on the cell can locally
distort individual eye and Channel.

And then in return you get a whole set of
responses from which again tight coupling

between molecular atoms at some point
even the iron skating inside the cell

hold said biological response and
then to me from global forces so

tight coupling between different lengths
that makes it often very hard to

model adequately because this is going
what I see as a major challenge if

we'd like to really quantitatively
model to describe biological

processes make quantitative predictions
experiments and more like a biology

generally quantitative so you can measure
something yet this is from a biological

clock here are certain reporter is
expressed and you get a solution.

You can measure expression levels
amplitudes of these of the relations then

being and so on.

So you get all of that and

then if you look at what
the explanation for what you measure.

What you usually get is
something like this you are and

that is something you find often if you
look past any molecular biology textbook

you've got the patterns that explains
nicely what's going on but in many.

It's not quite what at least I as
a physicist would like to see for

me this is somewhat akin to explaining the
experiment at the Leaning Tower of Pisa or

just the picture of Newton and the Apple
two e you get the basic idea but it's

still in the law of gravity so perhaps
we can do a little better and really

make a quantitative prediction going back
aspire to first principles as they can.

So those are the big challenges
that I think of a bio of physics.

Now what I've picked here.

I'm interested in mechanics
on this nano scale here.

So or a cell here on the lawn a picture
here you see a lot of comma teen D.N.A.

wrapped around his tones.

So it's a very crowded very

complex environment and
that does not look at all like a test.

You'll have biochemist
often we've got the cell.

So we're interested in what do
we can if you're features in

here are forces acting on the D.N.A.
or discarding and so on.

What does that really
do to our biological or

a biochemical by a physical
process it's not in order

to really answer that question what's
of all of mechanics here on this scale.

You just start somewhere
that somewhere for

because this is very often
equation of motion and

fundamental equation of motion he has
a lot of operations inside the fair.

Everything is really dominated
by discus two legged inertia

doesn't matter mass doesn't matter.

So all the laws the T. Times fiction
queer fish and it's really the fourth.

Plus in a hot and better environment here
we are not working at lower temperatures

in vacuum like in offices as
they do in the environment

it's them dominated in many
ways by Tommy fluctuation.

So we have.

Here are some of the random
forces stemming from

just the problem in motion that we need
to put into our equation of motion.

So that's the basic inclination of motion
to describe the physics that we that we

need to look at and to be in our interest
in our it is going to be can exceed

how this year we describes and affects
biological function couple of caviar.

This is sort of standard statistical
mechanics statistical mechanics

most of the difficult mechanics is
at some of the Nemechek Librium but

show me a stellar thermodynamic it
would be a death cell generally not

deliberate on give you later an example
of actually see this happening.

Fortunately for a living them statistical
mechanics have made tremendous

progress over the last decade or so.

So hopefully they'll get more
of that really to get better

describe non-lethal Abrahm situations.

Another problem is.

The typical chemical description the that
you often see reaction kinetics and so on.

You talk about concentration etc And
when you talk about concentration.

You are talking about a very big on
somebody here usually However you have

only a few molecules often for
certain D.N.A.

binding Portie in Conception factors or
cell in bacteria send maybe five copies.

So all these descriptions here in terms of

concentrations become problematic
when you have only five molecule it's

what does the concentration mean in such
a case I have to be very cautious young.

In physics.
Generally we have sort of the two body

problem we have solved the many body
problem that's statistical mechanics but

the somebody problem is usually somebody
else's problem and not as well.

Tweeted.

So those are what I see here
is the difficulties that we're

dealing with no one.

We do about that.

Let me give an example here how we can
use statistical mechanics to describe

a biological object very simple
one year just the D.N.A.

molecule The first is the of
a simple D.N.A. molecule and

so I'm a physicist by training somebody
in a molecule really my model of D.N.A.

is merely that much this year I'm
assuming what I am and if you want

to know the elasticities of this
swinging What are we can just put on it.

So initially it assumes a random quarter
in water and then we can just and

whatever that core in here put on it.

Measure its elasticities.

The important point here is

what we're looking at when we do this
they're looking at purely in topic for

the spear not pulling on any
chemical bonds or anything yet.

Just what we're doing is the system out
of a confirmation shock and to enter.

Get as many possible confirmations top
confirmation where in the extreme case

that has only one possible confirmation
that it's a big difference and

Toppy between this state and
the states here.

And that gives nice then the difference
in the energy difference and

the energy means different
then we store in Forth.

That puts a comet as my D.N.A.
quite nicely.

Again we can measure that extension first.

With a month over fifteen years ago
they got cross extension curves and

so on one thing you can get fairly quickly
of that as a characteristic posterior

characteristic profiteer interesting how
much force to actually need here too and

whether these things is
characteristic energy for and topic.

Anything is K.B. T.
characteristic length scale.

It's what's called the persistence
length of the D.N.A.

So the length scale on which D.N.A. can
actually bend is the relevant links scale

here and that's about fifty nanometers so
collectivistic for.

Scale eighty phantom you wouldn't
say just very very little know

it later back to this.

This is on the cellular phone so
they got these products tension.

And then.

Well of course you compare if you get
a curve like this you compared to feel

where you find had

to change it so those models have been
around for probably about fifty years.

I mean what's so hard about
counting confirmations for each and

up and to and distance and
when they make the comparison you know as

it turned out it didn't fit and back then.

Well what do you do come up
with all kinds of reasons but

it didn't fit all of them
presumably experimentally.

Maybe something is wrong with the D.N.A.
here D.N.A.

is not really a good model polymer has all
these sequences depend features in there.

It's not really a home or polymer and saw
that that paper is full of these kind of

speculations as it turns out there
was something wrong with the field.

We basically what they put in that

forgotten bottle that even within one

segment of the D.N.A. for one of those
persistence things long segments.

You also have some thermal fluctuations so
it's.

You can't just model it as
basically joined jointed what.

But you have fluctuations within
if you do that by to get to what's

called the bond like chain
model from going to jail and

here compared to one of our
measurements everything is bang on.

So if you can for some of fluctuations
correctly everything fell

just nicely in place again and
about as good again.

So good to use that to
calibrate our instrumentation

dollars I think to calibrate
our optical tweezers.

We just measure a long piece of D.N.A.

the other facility and we can calibrate
our instrumentation that that point.

So that's what you can do here just
another example of what you can

do with these optical tweezers for
instance he have a D.N.A.

molecule a long one between two
microspheres we can play around with it.

We can stretch as we can even tire
not into it as some all about it

many years ago.

So here we have a bit of a knot we can
pull it tight open it up again and

see if a little hard to see here
is a somewhat grainy image but

here you can see the knot in the D.N.A.
molecule.

So those are the kind of manipulation
techniques that we have available and

of course now you can do a lot of
interesting polymer physics with it.

Look at dynamical properties of the D.N.A.
molecule hydrodynamic

interactions mechanical constraints and
a couple of other things here.

We did some of that sort of and
with overview of some of those things

that we did relaxation time of
a stretched in a molecule and

basically what we found is that
most really behaves like and.

Over that.

Not like an over them violence to being so

you put on this thing if you
pull hard on it and then.

Pitch goes up so or

relaxation times get shorter in
the constitutional transfers the way.

All of that worked out just fine.

And feel we could pretty much predict
this year just by knowing the person.

The only adjusts the only parameters when
he goes in these things is persistence

things of the IN A BIT was reasonably well
known and also we could extract the first

bit more interesting the friction core
fission of the D.N.A. molecule and

if we did that actually get some measure
of logic to know how to name a correction

to plants worth a hundred and they
make corrections and what we found was

basically we just plug in the numbers
the dimension C. into the equations for

the friction coefficient of
a macroscopic longitudinal or

twenty first which is what we have fairly
close to what we actually measure.

So even.

Macroscopic hydrodynamics too good for
here or D.N.A.

molecule is just about
to never be the source.

Diameter rocks are just fine so.

So far everything good but.

It's interesting polymer physics but
what about biological relevancy of

everything that I just showed you was done
with long D.N.A. molecule with D.N.A.

sixteen microns long sometimes
even lend a dime of even longer.

But that's not the picture that we
have in the living cell I showed you.

It's up to scuttle earlier everything is
packed and tightly wrapped up as best

it can on the length scale maybe
a few persistent things are so on and

so know all of a sudden other things
become very important into show you that

in a second and some of the data for
instance how do you constrain your D.N.A.

How do you hold your endpoints How does
tension factor here points and so on.

So all of those things all of a sudden
become quite dominant these end effects or

logical or the relevant D.N.A. you have to

know sequence or that's the sequence
effect curvature of the D.N.A.

that's quite well established you can put
in sequences that locally bent the D.N.A.

sequence depend elasticities
eighty softer than C.G.

You can also have if everything is

heavily constrained you can
have tension in the D.N.A..

You can have talks acting on the D.N.A.

and also beyond just fluctuating
environments or thermal fluctuations

I already showed you a little bit of that
giving rise to topical of the city but

there are a thumber fluctuations a living
cell is there's a lot of action going on

with someone like your motor was pulling
on it all the time tugging on it you're

going to inscription doing application and
whatever else is going on inside the cell.

So you have a whole lot more going on
there than just some effect relations.

So we need to look a little
more at those things.

So let's first go to shorten a molecules
to do and to come up with any answers they

have to go to lengths relevant comparable
here to so one hundred nine to be telling

skill or so and I mentioned
the optical tweezers you thought

a little bit in this picture where put
it on this movie where we put it on the.

Very tight the not into the D.N.A.

you move to a big Michael sphere
typically micron in diameter.

And then move it around in the focal
plane of your microscope and

that's just fine for
relatively long D.N.A. molecules.

But if you've got a really short ones and
one end down here and

you just move your sideways what you
get is the shorter you get all kinds of

artifacts to make with spheres that
they're never perfectly symmetric and

it gets very very hard to even you
get to be in a length of about and

Micron a shorter you wanted
to difficult is there.

So what we did was we said OK
let's just put it actually away

from it here like this and then also Or

there's another little complication
Ordinarily if you're trapped or something

that can make with fear an optical
potential you are sitting in the minimum

of locally a parabolic potential so that
means the force that you are applying.

Is then linear with extensions
of in hopes law here.

And if you wonder one look
at some certain situation.

If you like to have a constant force
instead of constant extension.

Then we need to go to a different scheme
where the force is the same no matter

where in the potential you are and
show you by example that this is

really importance of where the D.N.A.
here actually gets shorter at some point

you want to keep the force constant So
what we do is meet.

Then not in the focus of what you usually
do but somewhere in the linear region of

the optical potential or pick up
a little bit of scattering force just

from the photons from the laser beam
it at a bounce back of the micro spear.

So we have a couple of tweaks here to
really go to the short length scale.

And if we know let measure of the lake.

This is the of our D.N.A. here and then

what we get is that we calculate

we try to extract the parameter here
this effect something like an effect

of persistence length effective
electricity of our D.N.A. molecule and.

That's something that should
be just a material parameter

almost like a Young's modulus or so
should depend only on the material here.

So it should not depend on the length.

So if I look at let's say
a conventional macroscopic spring.

If I attach to strings of the same spring
constant same length to each other

a void spring constant is cut
in half solved that sum and

know if you do the same thing or
with our D.N.A. molecule it's here.

That's no longer the case if you go to
shorten a shot in a molecule this effect

of persistence lengthier as a measure for
it's different if they're from this year.

So this one here decreases quite a bit.

So that's what we what we see here.

So again if everything was if this was
an intensive Proviron meter like a young

modulus or so
we would just have a flat line.

But what we actually see is.

For the short in a molecule and

here we are talking about around
two persistence length or so

you see really a precipitous drop here in
the persistent strength of the D.N.A. and.

This has been has been seen before in
experiments where people buy tour.

Basically take D.N.A. and a certain
protein that can actually like get D.N.A.

together to make circuits like this and
just look at how easy is it to form

the circles trying to
find out back what's the.

Persistence length and then they came out
and they noticed something similar and

then we got all kinds of
somewhat crazy explanations.

Again along the lines of our D.N.A.

is not really a good polymer
in this short length scales.

A lot of the speculation at that point
on micro bubbles and everything.

So a lot of that needs to know about
our circulation experiments for

sure but I can certainly tell
you about our experiments.

What extent that perfectly and

it's all about on the way conditions
in our experiments and with that.

I mean this is really
the second top explains.

So this is it is determined
by how many thumb

remotes are available to the thing here.

When in fact you ate and
well if I have let's say if

I have open end one notes available
then if a pin down the N.C.R.

like this like this and the same if
you know take a short piece of D.N.A.

If we put it in the context of a long
a molecule the rest of the molecule here

imposes boundary conditions on
the molecule the potential effect of.

And that's a different situation than
if I had the ends completely flea or

if they had the ends completely
attached or something and

those changes and boundary conditions
we can go back and really model it and.

Actually did a little bit
of that modeling work and

that's what these lines here
are from this modeling about

just putting the boundary conditions and
correctly and if we do that

in the plea agreement reasonable
agreement here with the experiments.

So at this point what we see is
really we got to be in a short.

Of these short length scales here mostly
boundary conditions effect if you

come very close to each other.

You expect because of the two

data sets you're beat.

It's a bit different to most.

Of the conventional stretching
in the actual plane

out of the pocket flap here some of
our own work down here in that region.

It's very hard to completely but
get together there

is very little unhappy about that data
point at the moment it seems to fall.

We're supposed to part of it
was a crossover between August.

This is so

up here in the in the end long is
anything many persistence length

long where basically any thumb or any
modes that you pick up from the ends don't

matter any more then then you can really
say you're solidly in the long D.N.A.

regime and persistence then is a good
measure up where I left the city as

soon as these additional modes
from the end point start to

matter then you have to have to boy about
then and adjust your persistence things.

Accordingly every so
often empirical basis.

And so the C.S. then if you just want
to use the standard of patients for

the length of a for the left.

This is the fourth extension of a D.N.A.
molecule like form like a chain and

depending on what boundary
conditions you have and

you can just plug in
these lower numbers for

the persistence length still beautiful is
the one that chain modeled by the way.

So Or just wasn't just that
persistence lengthier to account for

these additional notes at the end.

So those are molecules

briefly talk about sequence
depend less the city.

What can we do or can we play with
that as well to put more eighty India

more three G. in one case they
have two hydrogen bonds between.

The bases in the other case if we so
shouldn't that be somewhat different.

And there's a little complication with
all of this and the complication is

that these sequences in particular
a rich regions tend to bend the D.N.A.

locally so
you end up with twenty pieces of D.N.A.

and you have to somehow decouple
the two effects from bending and form.

To sequence depending left this is
the effects of the we made some constructs

here that are basically that
are built on trying to compensate and

effects from curvature by going
out of here if we induce one bent

later and bend it backwards to compensate
for that invest that we could make D.N.A.

constructs here that are reasonably
have almost the same curvature if we

use some of these models for
whole sequence curves D.N.A.

We also when I'm on a gel and so on to
check that they look like they have bought

the same curvature everything panned
out started printing on them and we get

substantial differences here between
the eighty which and the C.G. which.

D.N.A. So again we can calculate and
persistence lengths scaling up to.

If this was infinitely long and
not just short of pregnant here and

we get reasonable numbers here that are so

in one case higher and one case lower
than the standard persistence then for

completely random D.N.A.
We also compare this to other measurements

of the same that if on one case your arm.

There is less This is the program that
US for D.N.A. has been extracted from.

I'm a database of in a porting
core Christers said here there is

if you have lots of structure of India

crystals of D.N.A. and porting in if
you have a very soft piece of D.N.A.

then you are partly get of all a very
large spread and or structure so

that if you have a very rigid piece
of D.N.A. all those structures for

those the D.N.A. should be looking more or
less the same and from this kind of splat

other groups have extracted this if
you come up with us from typically

D.N.A. that nucleotides
are trying nucleotides and

if you use these unless
this is the problem.

It doesn't take you late
after how stiff our D.N.A.

should be get numbers that
are not completely and

wheezed in the bill so everything here is
a little smaller than what we measure but

at least the difference
between eighty which C.G.

which is sort of in the sort
of in the wide ballpark.

Different completely different for
the D.N.A. sequence station experiments.

There are some that have actually used
their left this is the parameters.

We shouldn't have really
seen any difference.

So the more in line with the D.N.A.
protein called crystals.

So we think we can actually
tell here in Haiti

which are very different
elastic properties.

So that's all on the naked D.N.A.

So what about biological

problems that we can actually solve
the third what we're looking at here.

Is we're interested in gene expression
doesn't we can expect gene expression.

So we looked at a very moderate
system known for whole

gene expression of speculated in bacteria
and that's the lactose free press or.

In equalise basically how that works
is you have your D.N.A. you have two

specific banding sequences here and
then you have your party in binding to it.

Your precipice.

And when you find similar tenuously
to both landing sites here and

then the D.N.A.
inside that nucleus inaccessible for

twenty good genes out
there on a problem is.

Can't get in there anymore.

The gene is turned off and
if this year the spawn breaks.

Then it's open again.

Gene is on again.

So this is a very simple
regulatory scheme very very

characterized fairly ubiquitous usually
a bit more complicated than this.

In particular you carry out but
you have often have multiple

proteins point to different
operator sites on the D.N.A.

have to come together to form some
big complex to do something and so

we pick the one here that we
could find like a person equal I

don't know the mechanical features some
of those and sort of hinted at already

from the naked D.N.A. So sequence defend
curvature and the less the city effects.

So it does the sequence in your metaphor.

How easy it is to form
these the president.

We look heavenly attention in the D.N.A.
here.

So can a bit of tension in the D.N.A.

actually prevent the formation
of the snoops the answer.

Naturalists Yes I'll show you more of that
later but a lot of things also operate

alignment operators separations of how far
despite insights away from each other.

How are they here oriented with
respect to the double helix and so on.

So all of that we have plenty
of mechanical features.

How do they in the end affect.

Their logical function.

So let's start out with D.N.A.
looping and attention.

So that's what's driving
this new formation process

are fluctuations in the D.N.A. So when is
fluctuating and at some point or Puerto.

Get close enough to bind being

formed then some time it wakes up again
and the same thing starts over again.

So we're talking here about.

Basically thumb effect Nations Indian aid.

We already learned characteristic for
scale.

K B T divided by persistent strength
eighty phantom you wouldn't see so

that's very very very little on the other
hand into a cellular process the how

much thought as it take for instance
to lift the portion of my D.N.A. here.

Once it's bound to quickly out of ten
people Newtons is fairly typical there for

two orders of magnitude higher forces
required to rip it off once it's bound

compared to this topic forces here.

Or are if you ask for instance the D.N.A.

put them on a premise that
one scrapes the D.N.A.

Starforce what forces can that molecule
and that when it came out to exert here or

there or usually twenty twenty
people knew it was a typical number.

So again two orders of magnitude larger So

we're dealing with very very small for
the C.R..

And so
can be potentially a very very sensitive.

McCann isn't because if it takes millions
hundreds Fenton you wouldn't see

it to bias these fluctuations such that
the two operators never fight each Iraq.

We have a very very sensitive
mechanical switches.

So technically how do we do that again
playing with our axial constant force

optical tweezers in a molecule
to banding sides just like.

We just invent with a laser
here be applied with

these very very small forces here.

In the accident election and we just
see watch the protein bind shortening

the D.N.A. and bind again and
that will be seaport team

coming on porting coming off
closing loop opening and so on.

And here is not where it's important
that we have a constant force.

And that we're not sitting in
the bottom of our potential young

abayas the force would actually
go up once you're forms.

We'd like to keep this constant here.

So we're sitting here on on the linear
slope of our optical potential So

that's how we practically realize this.

So this evokes quite Belfour Well
if we short D.N.A. molecules and

books valid very low forces hundred twenty
wouldn't send tens of them to Newton's or

so something that you couldn't do.

Let's say with Active X.

seems that overlaps and using So
this is how that works.

Here are some of the results.

This is why our data unfiltered
just what we observe.

We just look at our might was going up and
down here and

once in a by the forms stays
down here wakes up again.

It mostly bounces up so here.

SO CLOSE TO CLOSE open again.

And so on so
that they can filter it a bit and

then we get these kind of traces here
which we can then extract lifetimes of

the here in this case of the state
of the loop state down here and this

here already tells us that this person
is extremely sensitive to small forces.

So at one hundred twenty you
wouldn't see from here to here.

You see up here the group is mostly
closed down here in that state.

Up until just dial in another hundred
Phantom of the group is mostly open.

So it's indeed very sensitive.

So looking at the lifetime distribution.

In this case of the looped
states of once a loop is formed.

No matter what the apply here on this
fourth scale here once the loop is closed.

It doesn't really care anymore
what we do here at least not and

on the hunt a phantom you
wouldn't scale laugh.

And distribution is the same but
the distribution of the lifetimes for

the new state.

So the time that it takes to form
a loop is dramatically depend on force.

So this is what we know what we get
can we understand that quantitatively

first we started out with some very
very simple polymath here we here.

Can we just model our loopier.

So look at the free energy here.

Can we just look at the difference in
free energy between those two situations.

What's the difference here about one is
the stretching energy in the D.N.A. here.

In F D N A here.

That's something we can easily calculate
from the bottom like chain model from

the force extension relationship then we
also have some free energy associated

with loops of some kind of bending energy.

Plus binding energy here from the party in
we don't know what that is at this stage.

But we have a pretty good idea that
it's not depend on tension because here

the loop is completely isolated
from the rest of the D.N.A. And

finally there's also something associated
here with bending the D.N.A. to get

a boundary conditions flight and that one
is depend on force but also on the angle.

That the of the boundary conditions
that the porting imposes on the D.N.A.

So we have all of that we can
run it through the formulas and

then just calculate what
we would expect how we

would expect the formation of a to
scale with or to drop here with.

Tension in the molecule and
at least we see hundred twenty witnesses

enough to really get
this down quite a bit.

However we always have to make some
assumption about these boundary conditions

here and that complicates it a little bit
because we don't really know the boundary

conditions we have crystal structure
that's for the just for the party in here.

And those crystal structure spectating
just with a short in a fragment in here.

You cannot.

The lies the whole thing with
such a big floppy D.N.A..

Piece doesn't crystallize So
what they did was they crystallized

just the porting with very
short justice finding.

Fragments young.

And then just to artistically
hear the best of the group and

said that the time has come on.

But there is no turning to after this.

And so let me just play
the despair you can have and

a loop like this you am where we have
our intuition of the tangent vector

third D.N.A. going through the protein
display coming out the other way or

you can have the perilous orientation.

So something like this you are in
a loop like this you know we come in.

This way and go out the same direction and

that's something we cannot tell without
having the intervening look there.

Can we take the thumb on what are perhaps

the first that we find
the kinetics a little bit.

I wouldn't worry too much
about this in the moment but

once we really have the full
biochemical rates of our somewhat

more complex kinetic scheme your we
can use our model to predict how

these new formation rates should scale for
the antiparallel and

the Paralympian one is the solid
line one is the dash line here and

in our case we think it's looks pretty
much like it's antiparallel do so

not the bandits there on
the science cover but

this other somewhat I
believe our version of it.

So now that's something we

found to not have any evidence

that there's actually tension D.N.A. in be
able to make this biologically relevant.

So far no one has been able to really
measure certainly not in bacteria

the tension of the D.N.A.
inside the living cell have

been a few hints at least one is.

It's noticed that.

The ideal group size to get
the best repression out of your

out of your new P.R. is.

Indeed around five hundred base pairs that
something one can easily also calculate

from these polymer models everything
matches up quite nicely but

when we don't we will.

It's much much smaller.

And that is something we can quite

nicely if you just assume that there's
a bit of constitutive tension India.

So if you say the D.N.A. is constantly
under a little bit of tension then smaller

groups get favored in this and
this would argue for something like half

of African wouldn't pick on you would
not sell inside living cells and

there's also not been
experiment as a measurement of

tension in the U.K. Arctic D.N.A. during
my tours this year and they came up with

something like a couple of hundred twenty
one so point two people Newtons or so.

So at least that is something
of the order that's relevant for

our thesis of one hundred twenty Newton
for scale is at least not completely and

we know can we do everything a little
bit more quantitatively After all

we are suspect waning make
a better model here for our D.N.A.

than just cooed problem a model
that I had early on so.

That a model here our former colleague in
mechanical engineering who was modeling

underwater cables for the Navy and
scared that one down by

one of magnitude and
then describe our D.N.A. and

so put in the constitutive.

We can put in the city ten so here.

We can make it sequence depend.

Can we can do a lot of things
with that model here and.

So and then actually so
wonder the simulation and

calculate calculate
equilibrium shaping of our.

D.N.A..

And come up with something here

in this case this is the other group
apology that we don't think it is but

we can basically put anything in
that we'd like to come up with it.

Librium shape and
we can order from the left.

This is the parameter get the bending
energy associated with forming

that kind of world.

So that's something we can get
from that model working model.

Yes Something thought

the dynamic more public not

frozen of the didn't go forward
to a good question here.

That's

not

OK

so this model here just this
whatever it's doing it.

Hopefully it upon spec in and in a second
whatever I saw from this model here

on this is a dynamic model.

And you know put it up.

OK back on track.

So this model.

What did gives you is elastic energy
here of the equilibrium shape but

as I told you when you're dealing
with this kind of that and

that problems you have to
also look at entropy Yup And

of course binding the D.N.A. to operate
outside skills a couple of them and

modes of thought entropy met us and they
have to put that into the model we can do.

Within this of a second step.

We have the equivalent shape.

Now we can calculate the normal modes.

But want equilibrium shape and
that then in turn gives can

give us the total free energy here
using something that's quite a J.

factor are so basically what
that is we can calculate what

is the concentration of one operator
at the site of the other here.

So this is something we can calculate
here go to the hematology and

of the loop D.N.A. and the D.N.A. and

then integrate of all the idea
that it has accessible to it and

then we can plug all
the constraints in there here and

of what angle it has to bind
to bear it has to bind and so

on and get this effect of concentration
and that we can relate back than just to

the bottom factor here to
the free energy of the system and

actually come up with a reasonable
number of them if you do that we

get barely a height to forming the snoops

Young off about seven
point seven K B T and

the other one to know on the other side
from our experiments what we can do is.

We can try to measure this barrier to
formations of just bending the D.N.A.

just to the point where it's just about
to latch on to the potty in your can also

try to relate that from
these fast data hyung

basically we just made a record
assumption to just say OK.

Sort of a third order polynomial.

And then use the commerce.

Approximation for meantime to first
passage over that hump young.

And if you do that what we
what we get here isn't.

Perhaps as an expression here for

the lifetime of the state
as a function of Forth.

And the secret science shouldn't be there.

So anyway and then we can use this year.

Inversely fitted to our data for

the lifetimes of the state
as a function of force.

Get there.
Tell you here.

Barry Hyde out of it on this.

Here we get seven point four
K B T I think it's almost too good.

The agreement here I'm actually
surprised that it worked that well but

we get actually barrier
to formation out of this

honestly a little bit surprised how
good our quantitative model here

is let me just talk about one other
thing that's closely related to it.

In Vivo I mentioned earlier we're
dealing with a lot of fluctuations

from all these active posters these and
so on in the living cell.

So the first step for us can be just some

Your latest in our experiments just shake
one entity of the D.N.A. and see how much

more likely is that to form groups and
the answer in a nutshell is yes we can.

So we added about the added bite noise.

A little it's a little bit more
complicated than this with all

the compliance in the system and so on but

the increase the fluctuations in
the D.N.A. here by about five percent or

increase something like an effective
temperature by five percent or

that I'm very reluctant to really dwell
too much on this temperature notion here.

Increase the factorizations by five
percent and B. W. formation rate so

this is and putting this into our barrier

moderate we can then go to a fluctuating
barrier model see what that does to it and

come up with a reasonable description
here that sort of the scraps and so

at a little bit of noise to the system
active noise here can actually

speed up the course of quite a bit and.

Where that is probably important
is because of the polling.

If you looked at my data earlier you saw
the new piece of Morton maybe half of

the time or so spent a lot of time in
the state where you can actually express

the gene on the other hand through
his regular toy schemes are very very

efficient if you actually measure the gene
expression of the gene that's controlled

by this piece of the in a here you can
easily get five hundred to a thousand fold

the passion just in
the simple scheme like this.

How can that be possible
if it's open half the time.

So something else is going on here.

So one possibility is to have a lot of
active fluctuations in the cells or

as soon as the see a breakdown.

It has a chance to get back together
because it's shaking so much so

that one possibility here right
now trying to answer the question

how much fluctuations active fluctuations
to be actually happen in a living cell.

So what we just started doing was doing
to us is correlated spectroscopy on

life equalize cells and what we see.

So what we do is we randomly florescent
the label of our D.N.A. here.

The future for us now fluctuate in and
out of this except Haitian volume here.

And so we see intensity fluctuations
in the fluorescent signal

look at coalition functions then and

what we see is quite a bit of
a difference between life and death.

So it's hundred hundred hertz and

slower we have actually quite
a bit of active fluctuations

in the life since then in the death
says something similar has been seen.

Also in the fact the skeleton they had
to cut off is more closer to ten hertz

and so we tend to play attribute
this to molecular Motors.

So in the south the skeleton
in medicine system are so

typically ten hertz is a relatively
good turn over weight for

those molecular Motors sample chaotic
Motors can be quite a bit faster.

So perhaps that's my view actually get
further down here in the time scale but

this is still very very
preliminary to just getting this.

Kind of data here.

We think there might be something
to this is to fluctuations.

Another thing as one
figure that does not show

nothing we trying to do is can we
actually observe new formation in vivo

we have just started playing wound
with D.N.A. quantum dot conflict and

particle twerking white now relatively big
construction big quantum dots at the end

inserted into big cells just to
get a bit of a principle here and.

So what we see on this is figure so
we put a D.N.A.

molecule to quantum dots get it
inside a living cell track then

the emission and first thing we know it's
this big difference between life and

death cells life cells all over
the place that sells well that.

Also we can look at diffusion
year of this of all construct.

And some most D.V.C. diffusive behavior
on very short time and then scales

up to fuse of behavior long scale it's
not really much of a surprise they are.

But we really are interested in
telling from these conflicts.

How much D.N.A.
is basically effectively in between them.

If you have or two.

D.N.A. or two quantum dots young.

So they're relatively
close to each other or

they are fairly far apart
of the group is open.

How can we tell.

Absolute distance measurements
into colorful essence my cost

could be a fairly Twinkie.

So we tried something else young and the
something is to look at correlations see

young correlations like close
very short link up between them.

The two markers the two quantum dots
move in a relatively correlated fashion.

If they have a loose linkage between them.

We have a different kind of correlation.

And so we look at relative correlation
correlation in the relative

motion and if we do that.

See quite a bit of a difference.

Between what the in a conflict
the ninety base fears and

the long are born about two hundred or
so short ones correlations.

So you have the short months here and

much more correlated than the long
ones we can at least we think

we can use this to if we had
changes to the changed length.

We would probably be able to tell
something here this year in the moment

can't do it yet but we're sort of
slowly getting there at least for

lifetimes of the order of seconds to tens
of seconds we should be able to do that

and we're still working on developing
better reporter conflicts and so on.

Before it can actually get inside
the single cell but you need to really go

inside the call and be a barking on those
pops right now so I was there at the end.

So I hope I've been able to convince
you that mechanics actually met us for

biological processes on the nano scale.

So it's not just a small test tube
complex mechanical entity with

lots of things going on very small
forces can have a big effect.

Hundred fifty Newtons was enough to
completely disrupt the formation of

these regulatory complexes
fluctuations matter are certainly

the farmer fact relations but
increasingly we

also think that the a thermal
fluctuations form molecule motorists and

hopefully been able to convince you that
with these some of these techniques of

the distilled physics we can actually put
all of these observations in context and

actually come up with quantitative answers
and make quantitative predictive models

for complicated biomolecular Porthos
this and with that and at the end would

like to acknowledge graduate students and
post-docs are blocked on this.

And also some of the collaborators
here worth us from vocation.

Well Perkins from engineering he made
this model that we've been using and.

Or biochemical collaborator Jason come
from the University of Maryland for

that and at the end of my talk.

This is just as well

as if it's inside.

So that we in the vacuum of
immobilized on the slight moving and

then bacteria is part of the Polish
pretty much filling the entire

affair of the period basically that back
your comment on filth the entire thing and

it is so well it is constrained in
multiple ways slightly inside the cell.

Not everything is known about it but

you have plenty of attachments
between the D.N.A. in the cell wall.

You have different topple logical domains.

Where the D.N.A. is with putting
in space sickly petulant self.

So it can fluctuates but

probably only on relatively short
short length scales for the most part

because both increasing you
have it by five percent.

If you jump all life.

Yes Or more like five percent.

If it's repairable.

Yes So we are not really done increasing
the physical temperature there

at fluctuations to the molecule
that would be the increase of

fluctuations in the molecule by
shaking it by about five percent

that's what the seed Willy
means because it's not you know

they're not twisting if you just take
one end of a somewhat longer D.N.A.

molecule enough to basically get
the relevant fluctuations between the OP.

They are taught to be about five percent
larger than what they are naturally just

stumbling through what
those five percent are like

so you start their eight year olds.

Yes Or
you say depending on this is not ours.

This is just one of God's.

Or speculating on this one.

This is a difficult one.

So the question was why did in
the civilization experiment

to measure the sequence depends that they
left the city not always ferment and

you have to appear for comparison by the
experiment but all of got scared are by

did they not really see a difference
then they had different youth.

So I'm not quite sure
what the reason there

is one thing is they didn't really make an
attempt to separate curvature from a left

this is the thought I don't think even
know what they actually thought of their

experiment if just necklace the things
somewhat cancelled or I don't know what.

Of course another thing is when
you go to disability smaller

groups you bend the D.N.A. very very hard.

We are not doing this we only
thought I would think at some point.

You would probably one engine only area.

And perhaps you and that machine
when you bend it very very hard.

You're really dominated by the two
phosphate points out there are just.

Basically when we put on things there.

Most of the cylinders and
topic which seem so

just this week fluctuations here with
me are much more sensitive to all.

What's happening really between the base
of the two or three hydrogen bonds and

we just look at these very big fluctuation
where stay when it happened to think very

hard that they're part of the most bump
up against a possible back on that of

the same no matter what the sequence
that's so that's the Earth and

this is the best I can come
up with at the moment that's.