Characterization of Chaotic Motion of DNA in Linear Shear Flows

2003 ◽  
Author(s):  
D. G. Walker ◽  
M. A. Stremler
Keyword(s):  
Self Assembly ◽  
Dna Hybridization ◽  
Shear Flows ◽  
Coarse Grained ◽  
Stable Limit ◽  
Flow Conditions ◽  
Wide Range ◽  
Linear Shear ◽  
Stable Limit Cycles

Motion of macromolecules in flows is important to several disciplines such as DNA hybridization studies, self assembly of nanostructures, and transport of suspensions. The present study simulates the motion of macromolecular structures in linear shear flows. A molecular chain is modeled as a coarse-grained series of beads and springs. For a wide range flow conditions, the flow appears chaotic, where quasi-stable limit cycles are observed for several smaller ranges of flow conditions.

Design and Characterization of Nanoarchitectures from Multifunctional Polyparaphenylenes

2003 ◽  
Vol 776 ◽  
Author(s):  
Renu Ravindranath ◽  
Suresh Valiyaveettil ◽  
Chinnapan Baskar ◽  
Ananda Putra ◽  
Fitri Fitrilawati ◽  
...  
Keyword(s):  
Thin Films ◽  
Conducting Polymers ◽  
Self Assembly ◽  
The Self ◽  
Morphological Properties ◽  
Synthesis And Characterization ◽  
Solution Properties ◽  
Wide Range ◽  
Modified Surfaces

AbstractConducting polymers are interesting materials due to their wide range of applications in electronics, sensing, photonics and display applications. The present paper delineates the synthesis and characterization of the three functionalized poly (p-phenylene)s (PPP) (A-C) and solution properties of the polymers. The self-assembly of the polymers were investigated on various substrates and the optical/morphological properties of thin films of these polymers were also studied. The spontaneous self assembly of the modified PPP's lead to the formation of thin films on both hydrophilic and modified surfaces.

scholarly journals Basin Hopping as a General and Versatile Optimization Framework for the Characterization of Biological Macromolecules

2012 ◽  
Vol 2012 ◽  
pp. 1-19 ◽  
Author(s):  
Brian Olson ◽  
Irina Hashmi ◽  
Kevin Molloy ◽  
Amarda Shehu
Keyword(s):  
Protein Structure ◽  
Structure Prediction ◽  
Optimization Problems ◽  
Protein Docking ◽  
Coarse Grained ◽  
Biological Macromolecules ◽  
Wide Range ◽  
Multiple Variables ◽  
Basin Hopping

Since its introduction, the basin hopping (BH) framework has proven useful for hard nonlinear optimization problems with multiple variables and modalities. Applications span a wide range, from packing problems in geometry to characterization of molecular states in statistical physics. BH is seeing a reemergence in computational structural biology due to its ability to obtain a coarse-grained representation of the protein energy surface in terms of local minima. In this paper, we show that the BH framework is general and versatile, allowing to address problems related to the characterization of protein structure, assembly, and motion due to its fundamental ability to sample minima in a high-dimensional variable space. We show how specific implementations of the main components in BH yield algorithmic realizations that attain state-of-the-art results in the context of ab initio protein structure prediction and rigid protein-protein docking. We also show that BH can map intermediate minima related with motions connecting diverse stable functionally relevant states in a protein molecule, thus serving as a first step towards the characterization of transition trajectories connecting these states.

Bioconjugates of Luminescent CdSe-ZnS Quantum Dots with Engineered Recombinant Proteins: Novel Self-Assembled Tools for Biosensing

2000 ◽  
Vol 642 ◽  
Author(s):  
Ellen R. Goldman ◽  
Hedi Mattoussi ◽  
Phan T. Tran ◽  
George P. Anderson ◽  
J. Matthew Mauro
Keyword(s):  
Quantum Dots ◽  
Recombinant Proteins ◽  
Self Assembly ◽  
Emission Spectra ◽  
Igg Antibody ◽  
Photo Degradation ◽  
Size Dependent ◽  
Near Ir ◽  
Wide Range

ABSTRACTColloidal semiconductor quantum dots (QDs) are luminescent nanoparticles with size- dependent emission spectra spanning a wide range of wavelengths in the visible and near IR. This property, as well as their higher resistance to photo-degradation compared to organic dye labels, makes QDs potentially suitable for certain biomolecule tagging and multiplexing applications. We describe an electrostatic self-assembly approach for conjugating highly luminescent colloidal CdSe-ZnS core-shell QDs with engineered two-domain recombinant proteins to form conjugates for sensing and imaging applications. The design, preparation, and characterization of high quantum yield IgG antibody-binding protein G bioconjugates using luminescence, electrophoretic gel shift, and affinity assays is reported.

scholarly journals Mesoscale Simulations of Polymer Solution Self-Assembly: Selection of Model Parameters within an Implicit Solvent Approximation

Polymers ◽  
2021 ◽  
Vol 13 (6) ◽  
pp. 953
Author(s):  
Juhae Park ◽  
Abelardo Ramírez-Hernández ◽  
Vikram Thapar ◽  
Su-Mi Hur
Keyword(s):  
Polymer Solution ◽  
Self Assembly ◽  
Shape Change ◽  
Coarse Grained ◽  
Model Parameters ◽  
Implicit Solvent ◽  
Scaling Exponent ◽  
Single Chain ◽  
Wide Range ◽  
Selection Of

Coarse-grained modeling is an outcome of scientific endeavors to address the broad spectrum of time and length scales encountered in polymer systems. However, providing a faithful structural and dynamic characterization/description is challenging for several reasons, particularly in the selection of appropriate model parameters. By using a hybrid particle- and field-based approach with a generalized energy functional expressed in terms of density fields, we explore model parameter spaces over a broad range and map the relation between parameter values with experimentally measurable quantities, such as single-chain scaling exponent, chain density, and interfacial and surface tension. The obtained parameter map allows us to successfully reproduce experimentally observed polymer solution assembly over a wide range of concentrations and solvent qualities. The approach is further applied to simulate structure and shape evolution in emulsified block copolymer droplets where concentration and domain shape change continuously during the process.

scholarly journals High-throughput microfluidic characterization of erythrocyte shape and mechanical variability

2018 ◽  
Author(s):  
Felix Reichel ◽  
Johannes Mauer ◽  
Ahmad Ahsan Nawaz ◽  
Gerhard Gompper ◽  
Jochen Guck ◽  
...  
Keyword(s):  
Mechanical Properties ◽  
Red Blood Cells ◽  
High Throughput ◽  
Blood Cells ◽  
Microvascular Blood Flow ◽  
Flow Conditions ◽  
Wide Range ◽  
Single Well ◽  
Good Agreement

The motion of red blood cells (RBCs) in microchannels is important for microvascular blood flow and biomedical applications such as blood analysis in microfluidics. The current understanding of the complexity of RBC shapes and dynamics in microchannels is mainly based on several simulation studies, but there are a few systematic experimental investigations. Here, we present a combined study, which systematically characterizes RBC behavior for a wide range of flow rates and channel sizes. Even though simulations and experiments generally show good agreement, experimental observations demonstrate that there is no single well-defined RBC state for fixed flow conditions, but rather a broad distribution of states. This result can be attributed to the inherent variability in RBC mechanical properties, which is confirmed by a model that takes the variation in RBC shear elasticity into account. This represents a significant step toward a quantitative connection between RBC behavior in microfluidic devices and their mechanical properties, which is essential for a high-throughput characterization of diseased cells.Significance StatementThe ability to change shape is crucial for the proper functioning of red blood cells under harsh conditions in the microvasculature, since their shapes strongly affect the flow behavior of whole blood. Our results from simulations and systematic experiments reveal the shapes and dynamics of red blood cells for different flow conditions and channel dimensions, generally in good agreement. However, in the experiments, cells do not exhibit a single well-defined shape for fixed flow conditions. We show that this distribution of shapes can be attributed to the variability in mechanical properties of red blood cells.

Exploring amyloid aggregates with coarse-grained protein simulations

2013 ◽  
Vol 1535 ◽  
Author(s):  
Philippe Derreumaux
Keyword(s):  
Self Assembly ◽  
Structure Prediction ◽  
Degrees Of Freedom ◽  
Coarse Grained ◽  
Amyloid Peptides ◽  
Cellular Environment ◽  
Amyloid Aggregates ◽  
Wide Range ◽  
Society Today ◽  
Dimension Number

ABSTRACTProteins are complex, yet elegant, machines fine-tuned by evolution to properly fulfill a variety of tasks in the crowded cellular environment. These are, however, very challenging numerically due to their dimension, number of degrees of freedom and the wide range of relevant time scales. With aging, some proteins misfold and form harmful amyloid aggregates associated with multiple neurodegenerative diseases, and in particular Alzheimer’s, which challenge our society today. Here, I present the coarse-grained OPEP (Optimized Potential for Efficient peptide structure Prediction) force field and what we can learn from OPEP simulations to get insights into the self-assembly of amyloid peptides.

scholarly journals Coexistence of chaotic attractor and unstable limit cycles in a 3D dynamical system

2021 ◽  
Vol 1 ◽  
pp. 50
Author(s):  
Dana Constantinescu ◽  
Gheorghe Tigan ◽  
Xiang Zhang
Keyword(s):  
Dynamical System ◽  
Limit Cycles ◽  
Algebraic Surfaces ◽  
Chaotic Attractors ◽  
Global Dynamics ◽  
Stable Limit ◽  
Invariant Algebraic Surfaces ◽  
Stable Limit Cycles ◽  
T System

The coexistence of stable limit cycles and chaotic attractors has already been observed in some 3D dynamical systems. In this paper we show, using the T-system, that unstable limit cycles and chaotic attractors can also coexist. Moreover, by completing the characterization of the existence of invariant algebraic surfaces and their associated global dynamics, we give a better understanding on the disappearance of the strange attractor and the limit cycles of the studied system.

Patterns in diversity and composition of the microbenthos of subarctic intertidal beaches with different morphodynamics

2020 ◽  
Vol 648 ◽  
pp. 19-38
Author(s):  
AI Azovsky ◽  
YA Mazei ◽  
MA Saburova ◽  
PV Sapozhnikov
Keyword(s):  
Species Abundance ◽  
Abundance Ratio ◽  
Wave Action ◽  
Coarse Grained ◽  
Sediment Properties ◽  
Β Diversity ◽  
Α Diversity ◽  
Wide Range ◽  
Similar Mode ◽  
Abundance And Diversity

Diversity and composition of benthic diatom algae and ciliates were studied at several beaches along the White and Barents seas: from highly exposed, reflective beaches with coarse-grained sands to sheltered, dissipative silty-sandy flats. For diatoms, the epipelic to epipsammic species abundance ratio was significantly correlated with the beach index and mean particle size, while neither α-diversity measures nor mean cell length were related to beach properties. In contrast, most of the characteristics of ciliate assemblages (diversity, total abundance and biomass, mean individual weight and percentage of karyorelictids) demonstrated a strong correlation to beach properties, remaining low at exposed beaches but increasing sharply in more sheltered conditions. β-diversity did not correlate with beach properties for either diatoms or ciliates. We suggest that wave action and sediment properties are the main drivers controlling the diversity and composition of the intertidal microbenthos. Diatoms and ciliates, however, demonstrated divergent response to these factors. Epipelic and epipsammic diatoms exhibited 2 different strategies to adapt to their environments and therefore were complementarily distributed along the environmental gradient and compensated for each other in diversity. Most ciliates demonstrated a similar mode of habitat selection but differed in their degree of tolerance. Euryporal (including mesoporal) species were relatively tolerant to wave action and therefore occurred under a wide range of beach conditions, though their abundance and diversity were highest in fine, relatively stable sediments on sheltered beaches, whereas the specific interstitial (i.e. genuine microporal) species were mostly restricted to only these habitats.

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.

Polymer Chemistry

2004 ◽  
Keyword(s):  
Conducting Polymers ◽  
Liquid Crystalline ◽  
Polymer Chemistry ◽  
Chain Growth ◽  
Crystalline Polymers ◽  
Wide Range ◽  
Cyclic Oligomers ◽  
Step Growth

Polymer Chemistry: A Practical Approach in Chemistry has been designed for both chemists working in and new to the area of polymer synthesis. It contains detailed instructions for preparation of a wide-range of polymers by a wide variety of different techniques, and describes how this synthetic methodology can be applied to the development of new materials. It includes details of well-established techniques, e.g. chain-growth or step-growth processes together with more up-to-date examples using methods such as atom-transfer radical polymerization. Less well-known procedures are also included, e.g. electrochemical synthesis of conducting polymers and the preparation of liquid crystalline elastomers with highly ordered structures. Other topics covered include general polymerization methodology, controlled/"living" polymerization methods, the formation of cyclic oligomers during step-growth polymerization, the synthesis of conducting polymers based on heterocyclic compounds, dendrimers, the preparation of imprinted polymers and liquid crystalline polymers. The main bulk of the text is preceded by an introductory chapter detailing some of the techniques available to the scientist for the characterization of polymers, both in terms of their chemical composition and in terms of their properties as materials. The book is intended not only for the specialist in polymer chemistry, but also for the organic chemist with little experience who requires a practical introduction to the field.

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