With thanks to @hugan.

Post from: NEQNET: Non-equilibrium Phenomena

248. Nature is not scale-free

Before I proceed to the (becoming usual already) list of posts published at NEQNET during the last two weeks, let me say a couple of words about the blog itself, which is currently the source of  my pride

1. First of all, the number of subscribers to our RSS feed has crossed the number 120 recently. I hope I didn’t disappoint you much, dear newcomers

2. NEQNET is now listed in DMOZ, open directory of the best internet cites around, together with such very popular blogs as Lubos Motl’s “Reference Frame“, “Cosmic variance” or its new host “ScienceBlogs“.

3. Probably because of the issues (1) and (2) the number of pageviews has reached yesterday 1200/day, while our Alexa Rank is now below 500000 (let me note that the transition from Alexa Rank 1900000 to Alexa Rank 500000 has happened in less than 2 months). Although it is a very long way to become as popular as “Reference Frame” (who currently has Alexa Rank around 120000), we will walk it together, you’ll see

4. I have finally discovered that StumbleUpon is able to send some decent traffic to the site

5. The last but the most important – NEQNET has finally ceased to be the blog of a single blogger. First of all, Jim Kotsybar decided not to be so shy as he was, and as a result – he was offered a space at NEQNET to share his poetry about physics and physicists with us. Please be nice to him, and you will find that he is great. Second, you are to see many new guest blog posts at NEQNET. By the way, if you want to share your thoughts about recent papers in arxiv or anything else related to science, please check out this page, you will be certainly welcome to make a guest post at NEQNET.

All of this happened during last two weeks. But enough self-advertisement… Just stay with us!

Physics

* Fun with energy gap for QCD Born-Oppenheimer Hamiltonian

I propose three different estimations for the mass gap in Born-Oppenheimer Hamiltonian for two heavy quarks. You are to decide which one is correct. Although the poll has come to the end, I am yet to present its results and explain what is the correct answer for the energy gap. Don’t worry, I remember about the poll

* Talk in Munich. Regularizing inflaton correlation functions

I explain how stochastic formalism shows that the infrared divergences in inflationary cosmology are getting regularized by effects of eternal inflation.

* On interaction between coherent condensate and turbulent flow in two dimensions

I discuss the interaction between coherent and turbulent flows in the upper layers of the atmosphere of the Earth.

* Where are the quarks in the Wilson loop?

I explain where quark operators are hidden in the definition of the Wilson loop and why it can be interpreted in terms of the quark path. This post appeared as a result of my conversation with one of you

* AdS/CFT and condensed matter applications

I decided to study what is behind attempts to describe high temperature superconductivity by AdS/CFT duality. I am left unhappy but then small research makes me happy again – some condensed matter can be indeed described by gauge theories.

* Talk in Munich. Regularizing correlator of curvature perturbation

I explain how to calculate correlation functions of the curvature perturbation from stochastic formalism and why these correlation functions are IR finite.

* From quarks to strings. On Liouville modes, instantons and confinement in Abelian theories

I discuss several physical ideas in the recent paper by Alexander Polyakov: Liouville mode and instanton picture of confinement in abelian QED.

* From quarks to strings. Migdal-Makeenko equation and AdS/CFT correspondence

I continue to discuss the recent Polyakov’s paper on string theory and quarks. The subject now is the loop equation, related technical difficulties and explanation why it may help for AdS/CFT studies.

* Ashtekar at Perimeter Institute

Abhay Ashtekar has recently visited PI. I briefly discuss his two talks – one about Big Bang singularity, another-about information loss in BH. Fascinating exchange with Lubos Motl in comments

* A question in general relativity and another poll

Jim Kotsybar (I am now willing to disclose it ) has asked a relativity-related question, and I would lke to know what my readers think The poll is closed now, and I have to present the correct answer.

* Non-gaussianity from postinflationary universe

I explain how topologically non-trivial defects contribute into the cosmic microwave background radiation observed by us.

* Multifield inflation on the landscape

A guest post by my friend Thorsten Battefeld from the Princeton U., who explains the mechanism of staggered inflation, that can be realized on string theory landscape.

* Cosmic strings – simple and nice introduction into the topic

I briefly discuss the recent introductionary review of cosmic strings by Achucarro and Martins.

Biology

* Synthetic biology and iGem: interview

I have interviewed the leader of the Russian team participated in iGem 07, international student competition in synthetic biology.

* Synthetic biology and iGem: part 2

In 2nd part of the interview, the leader of the Russian team in iGem 07 shares with us his thoughts on technologies of molecular cloning and the future of nanotechnology in Russia .

Poetry

* Melancholy

Jim Kotsybar has just sent me his another poem, which I liked very much (as usual) and would want to share it with you.

* Illuminated

James Kotsybar is offered space at NEQNET and joins its writers officially as a Singer of Physics.

Fun, Various

* Metamodern – trajectory of technology

Eric Drexler, the founding father of nanotechnology, just has made his blog public and I acknowledge this fact

* Fun with Amazon.com

As you know very well, Amazon.com is an incredible source of extremely valuable assets which can become yours with just one click (well… several clicks…). Let us find out what Amazon has to offer in Christmas season…

* Steven Chu is the secretary of energy

Nobel Prize Winner Steven Chu is going to become the Secretary of Energy. It is great to feel that I was wrong about Obama – he will listen scientists (and one of them – every single day).

* Google Books now include magazines

Google has just announced that it is going to include all issues of many magazines into the Google Books index.

Post from: NEQNET: Non-equilibrium Phenomena

140. First two weeks of December at NEQNET

D.: How did you check that your bacteria have the properties you wanted (in your case, that the reaction to the copper abundance is present)?

A.S.: This problem (one of the simplest ones) is not yet solved, since we did not present the working example of bacteria yet. Several elements in the Registry of Standard Biological Parts may work as effective indicators – corresponding sequences of genes encode fluorescent proteins. If you put such an indicator into the contact with regulator and turn the latter on, bacteria will become (if you highlight them with blue light) red or green colored in several minutes. Here is an example of the genetic sequence encoding indicator – http://parts.mit.edu/registry/index.php/Part:BBa_I13521. Using spectral methods, it is  easy to determine how much of a given color is present in the sample.

D.: How DNA fragments (BioBricks) are created in practice? How rapidly can they be synthesized? who was responsible for the actual DNA synthesis in iGem – the teams themselves or somebody else?

A.S.: In practice, it is very simple if you have the necessary equipment and ferments. We perform the synthesis ourselves (this is what represents the educational part of the project), the team working on synthesis includes 3 and 6 year undergrads.

If one has to explain the process in a few words… First, we “implant” required genetic material into bacteria (this part of the process is called genetic transformation). The operation is rather rude w.r.t. bacteria – no more than 1/1000000-1/10000 of their initial population survive, but the positive part is that we have lots and lots of them Transformed bacteria divide and amount of the genetic material rapidly increases (this part of the process is called molecular cloning). Then, one is supposed to extract the resulting DNA from bacteria, cut the DNA by special ferments (that is where we got stuck because we were unable to receive all necessary ferments in time), mix it up with other fragments of genetic code and glue them together using other ferments.

The BioBrick standard proposed by the iGem host is especially good since all the fragments are glued together in the way they are supposed to with 99% probability. Unfortunately,  this is not always so in real scientific research and applications. Short sequences are actually synthesized by commercial companies. After the synthesis and appropriate “wrapping” they are ready for cloning in bacteria.

All these things are very well known (and the technology – established) from 1970s. I would like to recommend the Watson’s book “Recombinant DNA” (containing all the nesessary material at the level understandable for a beginner).

As for the characteristic time scale of the synthesis process, construction of a single sample takes about 5 days (the length of the process is essentially determined by the fact that bacteria population requires sufficient time to grow).

D.: In Russia, some serious investments into nanotechnology are currently planned. To which degree, can synthetic biology be considered as an alternative to nanotechnology? From your point of view, is it possible to build an equivalent of nanoindustry on the basis of synthetic biology?

A.S.: You know, I am rather sceptic about nanotechnology and its possible applications – in particular, since virtually nobody is able to accurately explain what is nanotechnology and nanoindustry. My favorite joke is: nanotechnology is from technology, all what remains is propaganda There are many popular speculations of a general character, but when one turns to real achievements and perspectives of nanotechnology, there are not so many. In this situation, all money-lovers turned into experts in nanoscience, got their grants and currently keep doing what they were doing before. Because of that, I think, money invested in nanotechnology in Russia will be slowly (or not so slowly) dissloved in space and time without any noticeable result produced.

Synthetic biology is also very young and not well established branch of science (by the way, there is no single serious research group in Russia working on  synthetic biology and its applications). However, its foundations related to genetic engineering, applied chemistry and bioinformatics seem much more solid to me.

From my point of view, the main advantage of artificial systems constructed by means of genetic engineering is that they use the natural life cycle, which is in harmony with the laws of thermodynamics (almost always forgotten by futurists lobbying nanotechnology). I think that is why the path of synthetic biology will more rapidly lead to some  practical applications. But this would be a good subject for a separate discussion.

D.: Would you like to give us a couple of comments regarding the project of Chinese team (who has won iGem 07)?

A.S.: The goal of the Chinese team was to construct bacteria able to differentiate – the title of their project was “Towards Self-differentiated Bacterial Assembly Line”. Differentiation is a process when initially homogeneous group of cells is separated (in space) into several groups of cells with very different properties. Differentiation is the necessary condition for the existence of any self-organization giving rise to a multicellular organism.

In bacteria, differentiation is a rather rare phenomenon (inherent to only some cianobacteria). Normal cells in E.coli are not differentiated, i.e., are all similar. This fact is not always convenient for biotechnology.

The Peking team has constructed two elements of the differentiation scheme that they have also proposed. Since the presentation is not uploaded to the iGem website (and I was not around during the Jamboree time), I am not sure whether they were able to actually construct differentiating cells.

Although the work of the Peking team was very good, I don’t feel that it was the most interesting. Personally, I liked the projects of the UC Berkeley team (artificial blood) and the team from Slovenia (by the way, the latter team is very strong – they were winners of  ‘06 competition) more.

D.P.: Thank you very much for the interview.

A.S.: I would like to thank the D. Zimin’s fund “Dynasty” who supported our project.

Instead of conclusion

Note that the Nobel Prize 08 was given for fluorescent proteins Alexej has discussed a bit above. It is clear to me now,  why indicators have made a revolution in molecular biology and genetics.

Slovenia also won the ‘08 iGem competition – indeed, the dream team. I would recommend you to take a closer look at the results table of iGem ‘08: it does contain some surprises – in particular, US universities did not do that well in the competition. No russian team has participated in iGem this year. Sad, probably, too much is invested in nanotechnology.

Post from: NEQNET: Non-equilibrium Phenomena

138. Synthetic biology and iGem: part 2

Browsing the web approximately a year ago , I have found an interesting article on wired.com which did show that biology students are considered somewhat more important asset than physics students nowadays – in particular, they are getting taught more effectively and more money is invested in their education  (the former, I guess, requires the latter, and yes, Ok, I am jealous )

If you decided not to click to the article in Wired, I’m talking about International (undergraduate!) student competition in synthetic biology iGem . First of all, what is synthetic biology?  Basically, today we know so much about how different micro-organisms (as well as their various parts) are functioning that we could try to engineer other, new, micro-organisms with properties that we want. The word “synthetic” in synthetic biology essentially means synthesis between biological science and engineering lore. Synthetic biology is a rather young actively developing (undeveloped?) branch of biology (the term itself was introduced in 1974) and without surprise it gets extremely popular among ambitious undergraduate and graduate students of faculties of biology, who want to make career in science as quickly and effectively as possible

As I said above, iGem is the international student competition in synthetic biology. Citing Wired,

The competition is a showcase for the burgeoning field of synthetic biology. Knight and his colleagues Randy Rettberg and Drew Endy, who created the contest in 2004, want to make biological systems easy to build by applying the tools of computer science and engineering: using standard parts and modular design to simplify complex systems. The goal is to create “genetic Legos” that could produce any chemical, from ethanol to pharmaceuticals.

In order to be accepted for the iGem competition, teams from different universities around the world were supposed to use the genetic repository at MIT (so called Registry of Standard Biological Parts) and construct a new genome of a bacteria having some interesting properties (maybe even useful in industry). For example, the team from UC Berkeley has created

… bacto-blood — an E. coli-hemoglobin mashup. The E. coli were engineered to produce hemoglobin – which carries oxygen to cells – and a chemical called trehalose. The trehalose made the cells able to withstand freeze-drying. Freeze-dried blood could come in handy in developing countries with limited refrigeration. It could be easily stored – just add (sterile) water when needed.

The idea of genetic Lego somewhat resembles Drexler’s nanobots with the only difference of the physical scale involved , so I immediately got interested in the subject and contacted the instructor of the Russian team in iGem 07 Alexej Skvortsov, associate professor in Biophysics Department, Faculty of Physics and Mechanics, St-Petersburg State Polytechnical University. He has kindly agreed to answer my naive questions about synthetic biology and iGem, see below (D. – me, A.S. – answers by Alexej). All mistakes you will find in the text are completely due to me being failure as a translator from Russian to English (the interview was initially conducted in Russian).

D.: What was the goal different teams at iGem have pursued -  did you have to present only a theoretical description of genome or was it necessary to construct real bacteria, i.e., represent “working” examples of the bacteria with required properties?

A.S.: To large degree, the iGem project is educational, i.e., its goal is to help team members to develop a better understanding of the principle of molecular genetics and methods of genetic engineering. In the ideal case, team was supposed to develop a theoretical basis for its project as well as to realize the project in practice. Thus, the answer to the question whether the given project is realizable played very important role.

According to the rules, we had to present our constructions in the BioBrick format and send them to the Registry in the form of DNA samples. Let me note that the Registry is more than just a website; in the beginning of the competition, every team receives a hard copy of the Registry, i.e., all the DNA samples you find on the website of the Registry. Each elementary block in the Registry is a DNA sequence in the form allowing its implantation into E.coli and subsequent reproduction. Presentation of a working example is very important and largely defines the outcome of the competition. Unfortunately, our team was unable to finish synthesis in time (June-October), because we did not receive ferments necessary for operations with DNA. We have bought ferments on summer, but have received only now, after the end of iGem – that is just a consequence of the fact that we are located in Russia. Nevertheless, now we are planning to construct developed details in the form of DNA.

Let me note that “genome” is an ensemble of all genes in a organism; our goal is much less ambitious than to deal with the whole genome, we are working with single genes having well-known properties. According to the synthetic biology concept, we do not need to know how are genes functioning and what is their fine structure; what we do need to know are their properties.

D.: How did your team develop your BioBrick? In particular, how did you figure out that a given DNA sequence is responsible for the detection of copper ions? (Alexej’s team has introduced a project of the bacteria which respond to high concentration of Copper ions in the medium.)

A.S.: To answer this question, I have to get into details of structure of a single gene. Any gene consists of promoter (defining whether the gene is turned on or off) and coding sequence (defining the outcome, the structure of the final product, for example, of a protein or a number of proteins). In bacteria, logic of gene organization is very precise, much more precise than, say, in mammals. In a sense, metabolism of bacteria is very close to perfect, and therefore it is much simpler to make genetic constructions in bacteria. One important feature of genes in bacteria is that promoter and coding sequence are not overlapped (as you remember, DNA is a long linear genetic text). As a result, it is possible to glue coding sequences of one genes and promoter parts of others (like in LEGO) in order to create new “genes”. I put parences here since the gene sequences were actually created by Nature, not by us. Our fragment  was represented by a single part from the Copper-dependent (at least supposed to be so) gene in E.coli.

Normally, this gene is activated (after a long sequence of events) when the concetration of copper ions in the medium grows. The gene also encodes pumping of copper ions away from the cell. We have found this genetic sequence from the NCBI open database analysing recent bibliography on effects of copper. We have supposed that the given sequence will activate any code that we substitute with the growth of copper concetration.

Let me also explain how we “cut” the sequence from the gene. Here a recent technological achievement has helped: DNA synthesis from the known sequence. You send te sequence (as a text) to a company, pay some money (in Russia – of the order of 1 EUR per single letter)  and receive the DNA sample in vitro. This is a common practice today – in a sense, it lays in the basis of synthetic biology – it is much more easier to synthesize short genetic sequences (less than 100 letters) rather than to cut them out of a DNA. iGem support team offers the DNA synthesis themselves, but it is of no use for us taking into account the delivery expenses.

To be continued.

Post from: NEQNET: Non-equilibrium Phenomena

137. Synthetic biology and iGem: interview

Physics

* Eternal inflation with many light scalar fields

As Adshead, Easther and Lim indicate, for N-flationary setup stochastic inflation regime is not the same as the regime of eternal inflation.

* Confinement. Extremely naive introduction

This is a very brief non-technical introduction into the problem of quark confinement, as the title indicates

* Criteria of confinement. Wilson loop – physical introduction

I am starting to discuss criteria of confinement. This time I explain why the area law for the behaviour of the Wilson loop corresponds to confinement.

* Criteria of confinement. Wilson loop – getting more technical

I continue discussion of the Wilson loop and this time calculate directly its behaviour for long contours in the confining phase of the pure gluodynamics.

* How stringy is QCD string?

I calculate the characteristic length of the QCD string and find than it is much larger than its thickness in both heavy and light quark limits. To my surprise, one of the most popular posts of the last two weeks

* Introducing doubt in Bayesian statistics 1 (guest post by Pascal Vaudrevange)

Pascal is explaining his recent paper with Trotta and Starkman about the introduction of doubt in Bayesian statistics.

* Talk in Munich. One interesting infrared scale in inflationary cosmology

This post is based on my talk in Munich. I am starting by identifying one interesting infrared non-perturbative scale in inflationary cosmology. Instanton immediately identifies it in comments as the scale of self-reproduction

* Talk in Munich. Two other interesting infrared scales

I present two other infrared scales which are interesting from the point of view of a cosmologist studying inflationary perturbations. This time Instanton is unable to idntify them

* Talk in Munich. Leading logs

I explain the genesis of leading logs in a self-interacting quantum field theory in de Sitter background.

* Hawking at PI

Isn’t it science news? It is announced that Stephen Hawking is relocated at Perimeter Institute (well, almost, for a part of a year currently).

* Recent lattice QCD simulations – how good is QCD in the infrared?

Recent QCD results reproduce correct spectrum of light hadrons with precision about 1%. We do not need to modify the QCD lagrangian in the IR.

Economics

* Rant: Big Bubble of the Housing Market

I discuss the US housing market turmoil, identify its origins and explain why the recent housing market bubble has led to the global financial crisis’ takeoff.

* World crisis – looking for a job?

According to the FED forecast, unemployment rate will reach 7.4% in November, highest in 14 years. From the beginning of this year,Americans lost about 1.2 million jobs in total. Do you, guys, want to discuss what is going to happen with jobs in science in forthcoming years?

* And to scare you even more…

Overall traffic (all US roads and streets) has dropped down 4.4% (equivalent to 10.7 billion vehicle miles) for September 2008 compared to September 2007. Although Lubos says, nothing like this is observed in Czechia

Fun

* Advice, by Jim Kotsybar

However one tries to advise, the results only antagonize, yet the moral that’s missed is to never insist that one’s own ideas are the most wise.

* New “Ender in Exile” by Orson Scott Card

I am glad to announce that Orson Scott Card has just released a new book in the Ender’s series – “Ender in Exile”!

* Two horror movies: one – Hollywood, another  – documental

I am briefly discussing two horror movies – one Hollywood and one documentary. I am to conclude that real life is so much more scary than any Hollywood movie:-)

* Japanese inventors are always ahead

I explain why the Soviets lost the patent wars to Japanese.

* But Korean inventors are sometimes ahead of Japanese…

Indeed so… as the following forthcoming mobile phone model proves, the creativity of Korean engineers is overwhelming!

Post from: NEQNET: Non-equilibrium Phenomena

118. Last two weeks of November on NEQNET

* Quintessence on the string theory landscape?

I discuss the recent paper by Kaloper and Sorbo explaining how quintessence can be realized on the string theory landscape, as follows from the title. The post also contains small introduction explaining what is quintessence field and why we want so hard to find it on the landscape

* Hard thermal loops: what is it?

I briefly explain what is hard thermal loop effective field theory.

* Leptophilic dark matter

I discuss the recent paper by Poppitz and Fox, where they introduce the model of dark matter that somewhat resembles Arkani-Hamed’s model.

* Belavin and Zamolodchikov on 2D quantum gravity

Belavin and Zamolodchikov study the correspondence between minimal 2D quantum gravity and p-critical one-matrix model.

* Unidentified extended sources of gamma ray emission

I discuss some unidentified sources of gamma ray emission recently found by H.E.S.S.

* A new theory of galaxy formation needed

It is claimed in the recent paper by Disney et al. that gaseous galaxies actually represent 1-parametric set. To explain it, a new theory of GF is needed.

* Second order hydrodynamic coefficients in some field theories (like QCD)

I am explaining how to calculate second order hydrodynamic coefficients in field theories and why we actually need to calculate them

* Quantum scale invariance on the lattice

As Shaposhnikov and Tkachev state, they have found a scheme leading to a non-perturbative definition of lattice field theories scale invariant on quantum level. Let us try and see whether this scheme works.

* One second order phase transition: video

Video of a second order phase transition. Can you guess what is the phase transition and what is the medium it happens in? Well, Lubos Motl and Theoreticalminimum have identified it as the one in supercritical . The phase transition is actually of higher order.

Biology

* Replication DNA in the cell

Just have found a very nice video explanation how DNA is replicated and wanted to share it with you… Enjoy

* Life cycle of stem cells

This video did help us to visualize how our baby is growing (Basically, the first stage of the human embryo growth is presented.)

Ramblings

* Academia: is it really a cult?

Does academia possess features of a cult? I discuss several pro- and contra- arguments. Featuring the Bug Girl in comments!

* So sorry, but I cannot help hacking Google Blog Search

This stupid hack did bring us about 25% of traffic we are enjoying now, but it did not came from the Google Blog Search

Post from: NEQNET: Non-equilibrium Phenomena

97. Second week of November on NEQNET

In the mean time, the number of subsribers to this blog has hit the magic number 100 (and peaked at 108 ) Thanks for subscribing, new readers, you are very much welcome!

Physics

* More talks: M2 branes and AdS/CFT, correlations of low multipoles in CMB

Igor Klebanov’ is talking on the membrane minirevolution at Perimeter; Glen Starkman argues that CMB is inconsistent with standard model of cosmology.

* Chaos in YM and confinement

I explain how relevant could be chaotic behavior of classical solutions of the Yang-Mills EOMs for the quantum YM at strong coupling. The maximal number of comments/post ever made on this blog.

* Chaos in quantum field theory

I discuss issues that may appear at quantization of classical theories that admit chaotic behaviour.

* A talk on scalar QFT, exact renormalization group and RG fixed points

I am trying to learn what is exact renormalization group. The main conclusion is that I don’t see how it can say anything new about UV structure of the theory compared to old poor Wilson RG.

* Watching worlds collide: bubbles, bubbles, bubbles

I discuss the paper by Matt Kleban et al. about collision of Coleman-de Luccia bubbles on the landscape and their effect on CMB.

* Edward Witten?s talk on 3D gravity

Edward Witten’s talk on 3D quantum gravity given at the Institute for Advanced Study. In comments Lubos explains why he thinks that monster group is irrelevant for extremal CFTs corresponding to .

Biology

*How eukaryotic cells feel direction

It is explained how the directional sensing in eukaryotic cells works; stochastic theory of the membrane reaction is introduced.

Politics and economics

* Excess of cash and origin of bubbles

I argue that the ultimate reason for bubbles to take off is the excessive activity on markets, when institutional and public investors have too much cash to invest.

* Obama is a president. What is there for us in it?

How Obama is going to deal with financial crisis and science/innovation funding? Let us see. Featuring Bee in comments!

Poetry

*Publishers and monkeys

James Kotsybar is trying to prove (using strong wording) that publishers are who they are.

Post from: NEQNET: Non-equilibrium Phenomena

89. First week of November on NEQNET

Often they contain other organelles such as mitochondria or chloroplasts, but this is not what will interest us at this time – let us focus on membranes.

Properties of these membranes are rather peculiar:  they actually represent a nice chemical compass. Concentration differences of certain chemicals between different sides of the membrane lead to its chemical polarization followed by the migration of the cell when these differences are at the level of few percent. This directional sensing is necessary, for example, for embryo development, and in fact, no multicellular organism can exist without it.

There is a known chain of chemical reactions that leads to directional sensing. The chemical factors that cluster on different sides of the membrane are called phospholipids PIP2 and PIP3. Two different enzymes can transform these lipids into each other. While phospholipids are bound to the membrane, enzymes can diffuse inside the volume of the cell. Enzymes become active only after they are getting absorbed by the membrane. Absorption of the first enzyme is activated by the extracellular signal (change of concentraction of the reactant inside the cell), and that is how the membrane feels the reactant. Absorption of the second enzyme is due to the coupling to PIP2, and that is how backreaction is introduced into the system.

After one understands this chain, one is ready to construct the quantitative theory of the membrane polarization. Suppose that is the radius of the PIP2 patch. This radius is essentially determined by the Langevin-type equation (we discussed the latter multiple times in the context of eternal inflation on this blog, as you will see in a monent, here we have a kind of eternal inflation of PIP2 patches inside the cell ):

,

where is the function of the concentration of one of the enzymes, is the linear tension of the interface with surrounding PIP3 phase and is the thermal noise. From the Langevin equation above one immediately derives the Fokker-Planck equation for the stochastic distribution of patches:

.

The physical picture is the following. The volume of different PIP2 patches grows stochastically, and eventually a single PIP2 phase survives, and its orientation determines the reaction of the cell to the external reactant. The process of patch formation is not actually very rapid, and so is the reaction of the cell. Since the mechanism of patch formation is diffusive, one gets the diffusive law of the form

,

and the corresponding time scale is the diffusion time essentially determined by the strength of thermal fluctuations. So, what your cells to be reactive? Heat them up

Post from: NEQNET: Non-equilibrium Phenomena

73. How eukaryotic cells feel direction