scholarly journals Circuit Topology for Bottom-Up Engineering of Molecular Knots

Symmetry ◽  
2021 ◽  
Vol 13 (12) ◽  
pp. 2353
Author(s):  
Anatoly Golovnev ◽  
Alireza Mashaghi
Keyword(s):  
Linear Chain ◽  
Distinct Group ◽  
Molecular Engineering ◽  
Cellular Functions ◽  
Structural Units ◽  
Chain Entanglement ◽  
Bottom Up ◽  
Circuit Topology ◽  
Conceptual Paper ◽  
Knotted Proteins

The art of tying knots is exploited in nature and occurs in multiple applications ranging from being an essential part of scouting programs to engineering molecular knots. Biomolecular knots, such as knotted proteins, bear various cellular functions, and their entanglement is believed to provide them with thermal and kinetic stability. Yet, little is known about the design principles of naturally evolved molecular knots. Intra-chain contacts and chain entanglement contribute to the folding of knotted proteins. Circuit topology, a theory that describes intra-chain contacts, was recently generalized to account for chain entanglement. This generalization is unique to circuit topology and not motivated by other theories. In this conceptual paper, we systematically analyze the circuit topology approach to a description of linear chain entanglement. We utilize a bottom-up approach, i.e., we express entanglement by a set of four fundamental structural units subjected to three (or five) binary topological operations. All knots found in proteins form a well-defined, distinct group which naturally appears if expressed in terms of these basic structural units. We believe that such a detailed, bottom-up understanding of the structure of molecular knots should be beneficial for molecular engineering.

Bottom-up Evolution from Disks to High-Genus Polymersomes

2018 ◽  
Author(s):  
Claudia Contini ◽  
Russell Pearson ◽  
Linge Wang ◽  
Lea Messager ◽  
Jens Gaitzsch ◽  
...  
Keyword(s):  
Self Assembly ◽  
The Self ◽  
Amphiphilic Copolymers ◽  
Chain Entanglement ◽  
Bottom Up ◽  
New Approach ◽  
High Genus ◽  
Transmission Electron ◽  
Minimal Radius ◽  
Stop Flow

<div><div><div><p>We report the design of polymersomes using a bottom-up approach where the self-assembly of amphiphilic copolymers poly(2-(methacryloyloxy) ethyl phosphorylcholine)–poly(2-(diisopropylamino) ethyl methacrylate) (PMPC-PDPA) into membranes is tuned using pH and temperature. We study this process in detail using transmission electron microscopy (TEM), nuclear magnetic resonance (NMR) spectroscopy, dynamic light scattering (DLS), and stop-flow ab- sorbance disclosing the molecular and supramolecular anatomy of each structure observed. We report a clear evolution from disk micelles to vesicle to high-genus vesicles where each passage is controlled by pH switch or temperature. We show that the process can be rationalised adapting membrane physics theories disclosing important scaling principles that allow the estimation of the vesiculation minimal radius as well as chain entanglement and coupling. This allows us to propose a new approach to generate nanoscale vesicles with genus from 0 to 70 which have been very elusive and difficult to control so far.</p></div></div></div>

Bottom-up Evolution from Disks to High-Genus Polymersomes

2018 ◽  
Author(s):  
Claudia Contini ◽  
Russell Pearson ◽  
Linge Wang ◽  
Lea Messager ◽  
Jens Gaitzsch ◽  
...  
Keyword(s):  
Self Assembly ◽  
The Self ◽  
Amphiphilic Copolymers ◽  
Chain Entanglement ◽  
Bottom Up ◽  
New Approach ◽  
High Genus ◽  
Transmission Electron ◽  
Minimal Radius ◽  
Stop Flow

<div><div><div><p>We report the design of polymersomes using a bottom-up approach where the self-assembly of amphiphilic copolymers poly(2-(methacryloyloxy) ethyl phosphorylcholine)–poly(2-(diisopropylamino) ethyl methacrylate) (PMPC-PDPA) into membranes is tuned using pH and temperature. We study this process in detail using transmission electron microscopy (TEM), nuclear magnetic resonance (NMR) spectroscopy, dynamic light scattering (DLS), and stop-flow ab- sorbance disclosing the molecular and supramolecular anatomy of each structure observed. We report a clear evolution from disk micelles to vesicle to high-genus vesicles where each passage is controlled by pH switch or temperature. We show that the process can be rationalised adapting membrane physics theories disclosing important scaling principles that allow the estimation of the vesiculation minimal radius as well as chain entanglement and coupling. This allows us to propose a new approach to generate nanoscale vesicles with genus from 0 to 70 which have been very elusive and difficult to control so far.</p></div></div></div>

Linear Chain Bis(α,β-dionedioximato)metal Compounds of the Nickel Triad: Solid State Design by Molecular Engineering

1977 ◽  
Vol 32 (5) ◽  
pp. 516-527 ◽  
Author(s):  
H. Endres ◽  
H. J. Keller ◽  
R. Lehmann ◽  
A. Poveda ◽  
H. H. Rupp ◽  
...  
Keyword(s):  
Solid State ◽  
Linear Chain ◽  
Mixed Valence ◽  
Structural Data ◽  
Molecular Engineering ◽  
Complex Molecules ◽  
Metal Compounds ◽  
Metal Interactions ◽  
Wide Range ◽  
Metal Metal

Chemical and structural data of numerous bis(α,β-dionedioximato)metal(II) compounds are summarized. All of them crystallize in columns but principally two different kinds of molecular arrangements occur in the solids. In one phase the molecular planes are inclined to the direction of the linear metal chains with an angle different from 90°. This allows only indirect interactions between the metal ions via the ligand. (“M—L—M” stacking.) The other modification consists of molecules with their planes perpendicular to the M—M-chains. This form allows direct metal-metal contacts (“M—M” modification). Depending on a few molecular parameters a “M—L—M” or a “M—M” stacking is obtained upon crystallization. Since for those compounds which could be isolated in both modifications the M—L—M form has the higher density it is concluded that only stronger M—M interactions stabilize the less dense M—M forms.A wide range of metal-metal separations with a lower limit of 3.15 Å in mixed valence systems are found in different “M—M” compounds. In any case the intrachain metal-metal distances are reduced considerably upon oxidation of the bivalent complex molecules. The influence of “electronic” and “sterical” parameters of the complex molecules on the intermolecular metal interactions and on the type of columns in the solid state is discussed.

ChemInform Abstract: Linear Chain Bis(α,β-dionedioximato)metal Compounds of the Nickel Triad: Solid State Design by Molecular Engineering.

1977 ◽  
Vol 8 (30) ◽  
pp. no-no
Author(s):  
H. ENDRES ◽  
H. J. KELLER ◽  
R. LEHMANN ◽  
A. POVEDA ◽  
H. H. RUPP ◽  
...  
Keyword(s):  
Solid State ◽  
Linear Chain ◽  
Molecular Engineering ◽  
Metal Compounds

scholarly journals Polynomial Invariant of Molecular Circuit Topology

Symmetry ◽  
2021 ◽  
Vol 13 (9) ◽  
pp. 1751
Author(s):  
Alireza Mashaghi ◽  
Roland van der Veen
Keyword(s):  
Knot Theory ◽  
Linear Chain ◽  
Polynomial Invariant ◽  
Circuit Topology ◽  
Polynomial Invariants ◽  
Knot Invariants ◽  
Topological Framework ◽  
Critical Chain ◽  
Chain Entanglements ◽  
Different Parts

The topological framework of circuit topology has recently been introduced to complement knot theory and to help in understanding the physics of molecular folding. Naturally evolved linear molecular chains, such as proteins and nucleic acids, often fold into 3D conformations with critical chain entanglements and local or global structural symmetries stabilised by formation contacts between different parts of the chain. Circuit topology captures the arrangements of intra-chain contacts within a given folded linear chain and allows for the classification and comparison of chains. Contacts keep chain segments in physical proximity and can be either mechanically hard attachments or soft entanglements that constrain a physical chain. Contrary to knot theory, which offers many established knot invariants, circuit invariants are just being developed. Here, we present polynomial invariants that are both efficient and sufficiently powerful to deal with any combination of soft and hard contacts. A computer implementation and table of chains with up to three contacts is also provided.

scholarly journals A rhythmically pulsing leaf-spring nanoengine that drives a passive follower

2021 ◽  
Author(s):  
Mathias Centola ◽  
Erik Poppleton ◽  
Martin Centola ◽  
Julian Valero ◽  
Petr Sulc ◽  
...  
Keyword(s):  
Brownian Motion ◽  
Molecular Motors ◽  
Molecular Engineering ◽  
Dna Origami ◽  
Chemical Energy ◽  
Leaf Spring ◽  
Bottom Up ◽  
Second Tier ◽  
Dna Nanomachine ◽  
Efficient Transfer

Molecular engineering seeks to create functional entities for the modular use in the bottom-up design of nanoassemblies that can perform complex tasks. Such systems require fuel-consuming nanomotors that can actively drive downstream passive followers. Most molecular motors are driven by Brownian motion, but the generated forces are scattered and insufficient for efficient transfer to passive second-tier components, which is why nanoscale driver-follower systems have not been realized. Here, we describe bottom-up construction of a DNA-nanomachine that engages in an active, autonomous and rhythmical pulsing motion of two rigid DNA-origami arms, driven by chemical energy. We show the straightforward coupling of the active nanomachine to a passive follower unit, to which it then transmits its own motion, thus constituting a genuine driver-follower pair. Our work introduces a versatile fuel-consuming nanomachine that can be coupled with passive modules in nanoassemblies, the function of which depends on downstream sequences of motion.

scholarly journals Coloring Invariant for Topological Circuits in Folded Linear Chains

Symmetry ◽  
2021 ◽  
Vol 13 (6) ◽  
pp. 919
Author(s):  
Jose Ceniceros ◽  
Mohamed Elhamdadi ◽  
Alireza Mashaghi
Keyword(s):  
Algebraic Structure ◽  
Linear Chain ◽  
Protein Molecule ◽  
Mathematical Approach ◽  
Circuit Topology ◽  
Basic Circuit ◽  
Linear Chains

Circuit topology is a mathematical approach that categorizes the arrangement of contacts within a folded linear chain, such as a protein molecule or the genome. Theses linear biomolecular chains often fold into complex 3D architectures with critical entanglements and local or global structural symmetries stabilised by formation of intrachain contacts. Here, we adapt and apply the algebraic structure of quandles to classify and distinguish chain topologies within the framework of circuit topology. We systematically study the basic circuit topology motifs and define quandle/bondle coloring for them. Next, we explore the implications of circuit topology operations that enable building complex topologies from basic motifs for the quandle coloring approach.

scholarly journals Bottom-up design of de novo thermoelectric hybrid materials using chalcogenide resurfacing

2017 ◽  
Vol 5 (7) ◽  
pp. 3346-3357 ◽  
Author(s):  
Ayaskanta Sahu ◽  
Boris Russ ◽  
Norman C. Su ◽  
Jason D. Forster ◽  
Preston Zhou ◽  
...  
Keyword(s):  
Hybrid Materials ◽  
De Novo ◽  
Molecular Engineering ◽  
Hybrid Nanostructures ◽  
Bottom Up ◽  
Solution Processable

Molecular engineering at the organic/inorganic interface enables robust bottom-up design of solution processable p- and n-type hybrid nanostructures for thermoelectrics.

Surface Structure of Nucleated Animal Cells: Carbon Replicas

1967 ◽  
Vol 25 ◽  
pp. 120-121
Author(s):  
Robert M. Glaeser ◽  
Thea B. Scott
Keyword(s):  
Cell Surface ◽  
Surface Structure ◽  
Particle Diameter ◽  
Cellular Functions ◽  
Animal Cells ◽  
Replica Technique ◽  
Carbon Replica ◽  
Characteristic Particle ◽  
Cell Surface Structure ◽  
Carbon Replicas

The carbon-replica technique can be used to obtain information about cell-surface structure that cannot ordinarily be obtained by thin-section techniques. Mammalian erythrocytes have been studied by the replica technique and they appear to be characterized by a pebbly or “plaqued“ surface texture. The characteristic “particle” diameter is about 200 Å to 400 Å. We have now extended our observations on cell-surface structure to chicken and frog erythrocytes, which possess a broad range of cellular functions, and to normal rat lymphocytes and mouse ascites tumor cells, which are capable of cell division. In these experiments fresh cells were washed in Eagle's Minimum Essential Medium Salt Solution (for suspension cultures) and one volume of a 10% cell suspension was added to one volume of 2% OsO4 or 5% gluteraldehyde in 0.067 M phosphate buffer, pH 7.3. Carbon replicas were obtained by a technique similar to that employed by Glaeser et al. Figure 1 shows an electron micrograph of a carbon replica made from a chicken erythrocyte, and Figure 2 shows an enlarged portion of the same cell.

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