The energy landscape as a unifying theme in molecular science

2004 ◽  
Vol 363 (1827) ◽  
pp. 357-377 ◽  
Author(s):  
David J. Wales
Keyword(s):  
Potential Energy ◽  
Self Assembly ◽  
Energy Surface ◽  
Energy Landscape ◽  
Magic Number ◽  
Building Blocks ◽  
Coarse Grained ◽  
Coarse Grained Model ◽  
The Right ◽  
Molecular Science

The potential energy surface (PES) underlies most calculations of structure, dynamics and thermodynamics in molecular science. In this contribution connections between the topology of the PES and observable properties are developed for a coarse–grained model of virus capsid self–assembly. The model predicts that a thermodynamically stable, kinetically accessible icosahedral shell exists for pentameric building blocks of the right shape: not too flat and not too spiky. The structure of the corresponding PES is probably common to other systems where directed searches avoid Levinthal's paradox, such as ‘magic number’ clusters, protein folding and crystallization.

scholarly journals Simulations of the 2D self-assembly of tripod-shaped building blocks

2020 ◽  
Vol 11 ◽  
pp. 884-890
Author(s):  
Łukasz Baran ◽  
Wojciech Rżysko ◽  
Edyta Słyk
Keyword(s):  
Molecular Dynamics ◽  
Monte Carlo ◽  
Diffraction Pattern ◽  
Triangular Lattice ◽  
Self Assembly ◽  
Building Blocks ◽  
Coarse Grained ◽  
Coarse Grained Model

We introduce a molecular dynamics (MD) coarse-grained model for the description of tripod building blocks. This model has been used by us already for linear, V-shape, and tetratopic molecules. We wanted to further extend its possibilities to trifunctional molecules to prove its versatility. For the chosen systems we have also compared the MD results with Monte Carlo results on a triangular lattice. We have shown that the constraints present in the latter method can enforce the formation of completely different structures, not reproducible with off-lattice simulations. In addition to that, we have characterized the obtained structures regarding various parameters such as theoretical diffraction pattern and average association number.

scholarly journals Energy Landscapes, Self-Assembly and Viruses

2005 ◽  
Vol 6 (2) ◽  
pp. 107-110 ◽  
Author(s):  
D. J. Wales
Keyword(s):  
Protein Folding ◽  
Potential Energy ◽  
Potential Energy Surface ◽  
Self Assembly ◽  
Energy Surface ◽  
Genetic Material ◽  
Magic Number ◽  
Molecular Beams ◽  
Energy Landscapes ◽  
Guided Exploration

Phenomena such as protein folding, crystallisation, self-assembly, and the observation of magic number clusters in molecular beams are all the result of non-random searches. Analysis of the underlying potential energy surface may provide a unifying framework to explain how such events occur as the result of a guided exploration of the landscape. In particular, icosahedral shells composed of 12 pentagonal pyramids are found to be thermodynamically favourable and kinetically accessible when the pyramids are not too spiky and not too flat. Hence, viruses with icosahedral capsids not only minimise the genetic material required to encode the repeated subunits, but may also utilise the favourable properties of a potential energy surface that effectively directs self-assembly.

Optical vs. chemical driving for molecular machines

2016 ◽  
Vol 195 ◽  
pp. 583-597 ◽  
Author(s):  
R. D. Astumian
Keyword(s):  
Potential Energy ◽  
Potential Energy Surface ◽  
Thermodynamic Parameters ◽  
Energy Surface ◽  
Molecular Machines ◽  
Coarse Grained ◽  
Power Stroke ◽  
Microscopic Reversibility ◽  
Single Time ◽  
External Modulation

Molecular machines use external energy to drive transport, to do mechanical, osmotic, or electrical work on the environment, and to form structure. In this paper the fundamental difference between the design principles necessary for a molecular machine to use light or external modulation of thermodynamic parameters as an energy sourcevs.the design principle for using an exergonic chemical reaction as a fuel will be explored. The key difference is that for catalytically-driven motors microscopic reversibility must hold arbitrarily far from equilibrium. Applying the constraints of microscopic reversibility assures that a coarse grained model is consistent with an underlying model for motion on a single time-independent potential energy surface. In contrast, light-driven processes, and processes driven by external modulation of the thermodynamic parameters of a system cannot in general be described in terms of motion on a single time-independent potential energy surface, and the rate constants are not constrained by microscopic reversibility. The results presented here call into question the value of the so-called power stroke model as an explanation of the function of autonomous chemically-driven molecular machines such as are commonly found in biology.

EXPLORING THE ENERGY LANDSCAPE

2005 ◽  
Vol 19 (15n17) ◽  
pp. 2877-2885 ◽  
Author(s):  
DAVID J. WALES
Keyword(s):  
Potential Energy ◽  
Potential Energy Surface ◽  
Rate Constants ◽  
Energy Surface ◽  
Energy Landscape ◽  
High Dimensional ◽  
Global Minima ◽  
Structure Dynamics ◽  
Recent Advances ◽  
Dimensional Object

Calculations of structure, dynamics and thermodynamics in molecular science all rely on the underlying potential energy surface (PES). Recent advances allow us to visualise this high-dimensional object in a compact fashion, locate global minima efficiently, and sample multistep pathways to obtain rate constants. These methods have been applied to a wide variety of systems, including clusters, glasses and biomolecules, and enable us to treat dynamics on the experimental timescale and beyond.

Dissipative Particle Dynamics Studies on the Self-Assembling Dynamics of the Peptide Amphiphiles

2008 ◽  
Vol 1135 ◽  
Author(s):  
Taiga Seki ◽  
Noriyoshi Arai ◽  
Taku Ozawa ◽  
Tomoko Shimada ◽  
Kenji Yasuoka ◽  
...  
Keyword(s):  
Self Assembly ◽  
Dissipative Particle Dynamics ◽  
Particle Dynamics ◽  
The Self ◽  
Peptide Amphiphiles ◽  
Coarse Grained ◽  
Coarse Grained Model ◽  
Self Assembling ◽  
Micro Structures ◽  
Good Agreement

ABSTRACTA coarse-grained model of peptide amphiphiles (PA) dissolved in aqueous solution was presented, where the effects of PA concentration, temperature and shear stress upon the self-assembly of PA were numerically studied by dissipative particle dynamics (DPD) simulation. We technically investigate the repulsion parameter aHW which indicates the repulsion force between the hydrophilic head of PA and water molecules, hence, at the same time, indicating the change in temperature. It was found that aHW played an important role in the self-assembly dynamics and in the resulting micro-structures of PA. By imposing shear strain on the simulation system, the formation of wormlike PA micelles was accelerated. The simulation results were in good agreement with our previous experimental results and the mechanism of shear-induced transition was proposed.

Application of a coarse-grained model for the design of complex supramolecular networks

2020 ◽  
Vol 5 (2) ◽  
pp. 484-492 ◽  
Author(s):  
Ł. Baran ◽  
W. Rżysko
Keyword(s):  
Self Assembly ◽  
Coarse Grained ◽  
Coarse Grained Model ◽  
Supramolecular Networks

Examples of self-assembly of molecules with different architectures.

scholarly journals Self-assembly of short DNA duplexes: from a coarse-grained model to experiments through a theoretical link

Soft Matter ◽  
2012 ◽  
Vol 8 (32) ◽  
pp. 8388 ◽  
Author(s):  
Cristiano De Michele ◽  
Lorenzo Rovigatti ◽  
Tommaso Bellini ◽  
Francesco Sciortino
Keyword(s):  
Self Assembly ◽  
Coarse Grained ◽  
Dna Duplexes ◽  
Coarse Grained Model
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