Rational design of patchy colloidsvialandscape engineering

2018 ◽  
Vol 3 (1) ◽  
pp. 49-65 ◽  
Author(s):  
Andrew W. Long ◽  
Andrew L. Ferguson
Keyword(s):  
Free Energy ◽  
Self Assembly ◽  
Rational Design ◽  
Energy Landscape ◽  
Building Blocks ◽  
Inverse Design ◽  
Free Energy Landscape ◽  
New Approach ◽  
Self Assembling

A new approach for inverse design of self-assembling building blocks by rational sculpting of the underlying self-assembly free energy landscape.

Factors Affecting Molecular Self-Assembly and Its Mechanism

2012 ◽  
Vol 9 (1) ◽  
pp. 43 ◽  
Author(s):  
Hueyling Tan
Keyword(s):  
Self Assembly ◽  
Building Blocks ◽  
Molecular Engineering ◽  
Molecular Structures ◽  
Polymer Science ◽  
New Approach ◽  
Factors Affecting ◽  
Dna Structures ◽  
Self Assembling ◽  
Wide Range

Molecular self-assembly is ubiquitous in nature and has emerged as a new approach to produce new materials in chemistry, engineering, nanotechnology, polymer science and materials. Molecular self-assembly has been attracting increasing interest from the scientific community in recent years due to its importance in understanding biology and a variety of diseases at the molecular level. In the last few years, considerable advances have been made in the use ofpeptides as building blocks to produce biological materials for wide range of applications, including fabricating novel supra-molecular structures and scaffolding for tissue repair. The study ofbiological self-assembly systems represents a significant advancement in molecular engineering and is a rapidly growing scientific and engineering field that crosses the boundaries ofexisting disciplines. Many self-assembling systems are rangefrom bi- andtri-block copolymers to DNA structures as well as simple and complex proteins andpeptides. The ultimate goal is to harness molecular self-assembly such that design andcontrol ofbottom-up processes is achieved thereby enabling exploitation of structures developed at the meso- and macro-scopic scale for the purposes oflife and non-life science applications. Such aspirations can be achievedthrough understanding thefundamental principles behind the selforganisation and self-synthesis processes exhibited by biological systems.

Self-Assembly of Peptide Amphiphiles: Molecularly Engineered Bionanomaterials

2015 ◽  
Vol 1113 ◽  
pp. 586-593 ◽  
Author(s):  
Hamizah Shamsudeen ◽  
Huey Ling Tan
Keyword(s):  
Self Assembly ◽  
Building Blocks ◽  
Molecular Engineering ◽  
Molecular Structures ◽  
Significant Advance ◽  
Polymer Science ◽  
New Approach ◽  
Dna Structures ◽  
Self Assembling ◽  
Wide Range

Molecular self-assembly is ubiquitous in nature and has now emerged as a new approach in chemical synthesis, engineering, nanotechnology, polymer science, and materials. Molecular self-assembly has been attracting increasing interest from the scientific community in the recent years due to its importance in understanding biology and a variety of diseases at the molecular level. In the last few years, considerable advances have been made in the use of peptides as building blocks to produce biological materials for wide range of applications, including fabricating novel supra-molecular structures and scaffolding for tissue repair. Today, the study of biological self-assembly systems represent a significant advance in the molecular engineering and is a rapidly growing scientific and engineering field that crosses the boundaries of existing disciplines. Many self-assembling systems are range from bi-and tri-block copolymers to complex DNA structures as well as simple and complex proteins and peptides. The attractiveness of such bottom-up processes lies in their capability to build uniform, functional units or arrays and the possibility to exploit such structures at meso-and macroscopic scale for life and non-life science applications.

scholarly journals Characterizing the conformational free-energy landscape of RNA using single-molecule field-effect transistors

2022 ◽  
Author(s):  
Sukjin Steve Jang ◽  
Sarah Dubnik ◽  
Jason Hon ◽  
Colin Nuckolls ◽  
Ruben L Gonzalez
Keyword(s):  
Free Energy ◽  
Single Molecule ◽  
Time Resolution ◽  
Field Effect ◽  
Field Effect Transistors ◽  
Energy Landscape ◽  
Building Blocks ◽  
High Time ◽  
Free Energy Landscape ◽  
High Time Resolution

We have developed and used high-time-resolution, single-molecule field-effect transistors (smFETs) to characterize the con-formational free-energy landscape of RNA stem-loops. Stem-loops are some of the most common RNA structural motifs and serve as building blocks for the formation of more complex RNA structures. Given their prevalence and integral role in RNA folding, the kinetics of stem-loop (un)folding has been extensively characterized using both experimental and computational approaches. Interestingly, these studies have reported vastly disparate timescales of (un)folding, which has been recently in-terpreted as evidence that (un)folding of even simple stem-loops occurs on a highly rugged conformational energy landscape. Because smFETs do not rely on fluorophore reporters of conformation or on the application of mechanical (un)folding forces, they provide a unique and complementary approach that has allowed us to directly monitor tens of thousands of (un)folding events of individual stem-loops at a 200 μs time resolution. Our results show that under our experimental conditions, stem-loops fold and unfold over a 1-200 ms timescale during which they transition between ensembles of unfolded and folded conformations, the latter of which is composed of at least two sub-populations. The 1-200 ms timescale of (un)folding we observe here indicates that smFETs report on complete (un)folding trajectories in which relatively extended unfolded con-formations of the RNA spend long periods of time wandering the free-energy landscape before sampling one of several mis-folded conformations or, alternatively, the natively folded conformation. Our findings demonstrate how the combination of single-molecule sensitivity and high time resolution makes smFETs unique and powerful tools for characterizing the con-formational free-energy landscape of RNA and highlight the extremely rugged landscape on which even the simplest RNA structural elements fold.

Determination of Base Flipping Free Energy Landscapes from Nonequilibrium Stratification

2019 ◽  
Author(s):  
Xiaohui Wang ◽  
Zhaoxi Sun
Keyword(s):  
Free Energy ◽  
Energy Landscape ◽  
Sampling Technique ◽  
Umbrella Sampling ◽  
Energy Simulation ◽  
Nonlinear Dependence ◽  
Free Energy Landscape ◽  
Convergence Criterion ◽  
Base Flipping ◽  
Convergence Behavior

<p>Correct calculation of the variation of free energy upon base flipping is crucial in understanding the dynamics of DNA systems. The free energy landscape along the flipping pathway gives the thermodynamic stability and the flexibility of base-paired states. Although numerous free energy simulations are performed in the base flipping cases, no theoretically rigorous nonequilibrium techniques are devised and employed to investigate the thermodynamics of base flipping. In the current work, we report a general nonequilibrium stratification scheme for efficient calculation of the free energy landscape of base flipping in DNA duplex. We carefully monitor the convergence behavior of the equilibrium sampling based free energy simulation and the nonequilibrium stratification and determine the empirical length of time blocks required for converged sampling. Comparison between the performances of equilibrium umbrella sampling and nonequilibrium stratification is given. The results show that nonequilibrium free energy simulation is able to give similar accuracy and efficiency compared with the equilibrium enhanced sampling technique in the base flipping cases. We further test a convergence criterion we previously proposed and it comes out that the convergence behavior determined by this criterion agrees with those given by the time-invariant behavior of PMF and the nonlinear dependence of standard deviation on the sample size. </p>

The Perturbed Free Energy Landscape: Linking Ligand Binding to Biomolecular Folding

ChemBioChem ◽  
2020 ◽  
Author(s):  
fareed aboul-ela ◽  
Abdallah S Abdelsatter ◽  
Youssef Mansour
Keyword(s):  
Free Energy ◽  
Ligand Binding ◽  
Energy Landscape ◽  
Free Energy Landscape
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