Mesoscale Chemistry A Workshop Summary (2015) / Chapter Skim
Currently Skimming:
6 Computational/Chemical Processes in Self-Assembly
6 Computational/Chemical Processes in Self-Assembly
Pages 51-64
The Chapter Skim interface presents what we've algorithmically identified as the most significant single chunk of text within every page in the chapter.
Select key terms on the right to highlight them within pages of the chapter.
From page 51... ...
Designing proteins with specific three-dimensional structures by changing amino acid sequences so that they would then self-assemble into interesting mesoscale structures has been a long standing engineering challenge that has still yet to be solved. T he workshop's final session featured five presentations on how computation and chemistry can be brought to bear on the challenge of understanding self-assembly of mesoscale structures.
|
From page 52... ...
many proteins form dimers or trimers and creating a However, using the underlying principles of fusion product of two of these proteins, using symmetry that exist in nature, research teams such as genetic fusion to create a gene that codes for both the one headed by Yeates have recently developed components, is in principle creating a larger protein design strategies that are realizing success in that has the two natural interfaces needed to create designing protein molecules that self-assemble into bigger structures. mesoscale structures.
|
From page 53... ...
approaches. The idea here was to take one natural Coarse-grained models, Noid explained, can oligomer and use computational methods for simulate longer length scales and time scales than sequence design to introduce the second interface at atomic-scale models, and they can reach exactly the right geometry (King et al.
|
From page 54... ...
For example, it is possible to l r o coar se-graining, t down and bottom up. T down top d Top t tailor coarse-ggrained models for partic cular systemss entaiils taking an experime ental observ vation to a to focus efforts on essential feature of a system and e es m param meterize a cooarse-grained model.
|
From page 55... ...
He cellular microtubule, which he said not only has described a method, known as force matching, that interesting material properties, such as mechanical takes the forces generated by an atomistic model and stability, but the ability to control chemistry, the forces generated by a coarse-grained model and particularly the hydrolysis of guanosine triphosphate tries to minimize the difference between the two (GTP)
|
From page 56... ...
Thus, the and carotenoids, triggering a flow of excitons that aspect ratio controls the expression of facets, which travel to the photosynthetic reaction center, where controls the ligand binding density and, ultimately, ATP is generated, and then discussed how modeling the strength of the interactions between the various and simulation work has enabled his group to detail surfaces and the particles and shapes that emerge. the movement of molecules within the This illustrates how interaction patchiness and shape photosynthetic apparatus to enable photosynthesis to control structure (Ye et al.
|
From page 57... ...
This m method calcul lates the potential of w with 82 part ticles in the unit cell and with no e a o mean force and t n torque betwee two partic in the en cles interactions emerging fro the surro e om ounding fluidd midd of a sea o particles, an it can qua dle of nd antify how ( (Haji-Akbari et al.
|
From page 58... ...
. c complex unit cells and oth structures form with a her s seeinng for the first time that exp e e perimental p periodicity an order we beyond the range of nd ell t f capaabilities and siimulation cap pabilities for t these very interparticle forces and to use that in f o nformation too large systems are starting to o e e overlap so th we can hat d design for metastability.
|
From page 59... ...
an aside that these crystals are photoactive and could When inserted into liposomes, BAR domain be used to carry out chemical reactions. proteins such as amphiphysin and endophilin, all of She also discussed work leading to which have a cluster of positively charged amino reconfigurable colloidal clusters that she has been acids that interact with the negatively charged lipids doing with David Pine's group at New York of the cell membrane, can form some interesting University.
|
From page 60... ...
. Voth's group Drin 07, p dommain proteins w their helices, called N with N-BAR, or c calculated th free ene he ergy of binding at the e withhout their hel lices, called BAR becaus the N se m molecular sc cale and fou und that the ere is a 5- - minal helices are absent These si term t.
|
From page 61... ...
One of Voth's more coarse-grained model and perhaps to a graduate students noticed that string-like features mesoscopic theory in order to understand the effect can form even at the initial phase of remodeling at of that chemistry on the mesoscale structure." Voth high protein densities and that the formation of these said that this is not always the case and that many strings is much less when the helices are missing. successful modeling efforts start with the coarseThis led to simulations at much lower protein grained model.
|
From page 62... ...
asking the exact same questions: How do these Session moderator Garcia-Garibay noted that assemblies grow, how does nucleation occur, and one of the things about mesoscale phenomena that where do these processes lead once crystal growth the field often thinks about is emergent behavior, starts? Jim De Yoreo then asked how these modeling and he asked the panel if simulation and modeling approaches apply to biomineralization given that can address emergent behavior or are there they are run at very high densities and natural behaviors at the mesoscale that cannot be described systems operating at low volume fractions.
|
From page 63... ...
By map that state to a thermodynamic equilibrium-like definition, it is an emergent property of a system, system that has a free energy function. "Is there a she said, and understanding the role of entropy is a function that can describe your active system so that terrific opportunity.
|
Key Terms
This material may be derived from roughly machine-read images, and so is provided only to facilitate research.
More
information on Chapter Skim is available.