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

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.

2001 ◽  
Vol 707 ◽  
Author(s):  
R.T. Malkhasyan ◽  
R.K. Karakhanyan ◽  
M.N. Nazaryan ◽  
C. Sung

ABSTRACTThe self-assembling systems in nanoscale powders of crystalline MoO3 are disclosed. For the first time, the double linear chain aggregates of the MoO3 nanoparticles were revealed in nanoscale powders of MoO3, treated by vibrationally excited molecules of hydrogen. Double linear chain aggregates form a linear and an orthogonal supperlattices. Both the double linear chain aggregates and the supperlattices formed are being considered as self-assembling systems. The treatment of the powders by the molecules of hydrogen is a method of obtaining long self-assembling chains of inorganic materials and supperlattices on their basis.


2001 ◽  
Vol 704 ◽  
Author(s):  
R.T. Malkhasyan ◽  
R.K. Karakhanyan ◽  
M.N. Nazaryan ◽  
C. Sung

AbstractThe self-assembling systems in nanoscale powders of crystalline MoO3 are disclosed. For the first time, the double linear chain aggregates of the MoO3 nanoparticles were revealed in nanoscale powders of MoO3, treated by vibrationally excited molecules of hydrogen. Double linear chain aggregates form a linear and an orthogonal supperlattices. Both the double linear chain aggregates and the supperlattices formed are being considered as self-assembling systems. The treatment of the powders by the molecules of hydrogen is a method of obtaining long self-assembling chains of inorganic materials and supperlattices on their basis.


2016 ◽  
Vol 26 (01) ◽  
pp. 1650001 ◽  
Author(s):  
Guillaume Aupy ◽  
Anne Benoit

We consider the problem of scheduling an application on a parallel computational platform. The application is a particular task graph, either a linear chain of tasks, or a set of independent tasks. The platform is made of identical processors, whose speed can be dynamically modified. It is also subject to failures: if a processor is slowed down to decrease the energy consumption, it has a higher chance to fail. Therefore, the scheduling problem requires us to re-execute or replicate tasks (i.e., execute twice the same task, either on the same processor, or on two distinct processors), in order to increase the reliability. It is a tri-criteria problem: the goal is to minimize the energy consumption, while enforcing a bound on the total execution time (the makespan), and a constraint on the reliability of each task. Our main contribution is to propose approximation algorithms for linear chains of tasks and independent tasks. For linear chains, we design a fully polynomial-time approximation scheme. However, we show that there exists no constant factor approximation algorithm for independent tasks, unless P=NP, and we propose in this case an approximation algorithm with a relaxation on the makespan constraint.


2008 ◽  
Vol Volume 9, 2007 Conference in... ◽  
Author(s):  
Samuel Bowong ◽  
Jean-Luc Dimi ◽  
Jean-Claude Kamgang ◽  
Joseph Mbang ◽  
Jean Jules Tewa

International audience We present the recent results obtained for the within-host models of malaria and HIV. We briefly recall the Anderson-May-Gupter model. We also recall the Van Den Driessche method of computation for the basic reproduction ratio R0 ; here, a very simple formula is given for a new class of models. The global analysis of these models can be founded in [1, 2, 3, 5]. The results we recall here are for a model of one strain of parasites and many classes of age, a general model of n strains of parasites and k classes of age, a S E1 E2 · · ·En I S model with one linear chain of compartments and finally a general S Ei1 Ei2 · · ·Ein I S model with k linear chains of compartments. When R0 <=1, the authors prove that there is a trivial equilibria calling disease free equilibrium (DFE) which is globally asymptotically stable (GAS) on the non-negative orthant , and when R0 > 1, they prove the existence of a unique endemic equilibrium in the non-negative orthant and give an explicit formula. They provided a weak condition for the global stability of endemic equilibrium Le travail que nous présentons ici est un résumé de quelques résultats récents obtenus dans [1, 2, 3, 5] concernant les modèles intra-hôtes multi-compartimentaux. Il s’agit d’une analyse mathématique et globale des modèles intra-hôtes de paludisme et de V.I.H . Mais avant de présenter ces résultats, nous rappelons d’abord la méthode de calcul développée par Van Den Driessche[71] concernant le taux de reproduction de base R0 car c’est cette méthode qu’utilisent les auteurs dans leur analyse. Ces modèles sont dits de Anderson-May-Gupter dont le modèle original est considéré comme précurseur. Une formule simple est donnée ici pour le calcul de R0 dans les modèles étudiés. Les résultats que nous rappelons ici sont obtenus pour un modèle du paludisme à un génotype de parasites et k classes d’âge, le modèle général à n génotypes de parasites et k classes d’âge, un modèle S E1 E2 · · ·En I S avec une chaîne linéaire de parasites et enfin le modèle général S Ei1 Ei2 · · ·Ein I S avec k chaîne linéaire de parasites. Lorsque R0 1, les auteurs montrent qu’il existe un point d’équilibre évident, le DFE (Disease Free Equilibrium) qui est GAS (globalement asymptotiquement stable) sur l’orthant positif. Lorsque R0 > 1, ils montrent l’existence d’un unique équilibre endémique dans l'orthant positif et moyennant une petite condition ils montrent que cet équilibre est globalement asymptotiquement stable.


iScience ◽  
2020 ◽  
Vol 23 (9) ◽  
pp. 101492
Author(s):  
Anatoly Golovnev ◽  
Alireza Mashaghi

2014 ◽  
Vol 28 (05) ◽  
pp. 1450039 ◽  
Author(s):  
Mark I. Gorenstein ◽  
Walter Greiner

The dipole–dipole interactions may lead to the linear chain formation in the ferrofluids. When the dipolar interaction energy is much larger than the thermal energy, the average length of the chains 〈n〉 becomes much larger than 1. This strongly influences on the magnetic susceptibility χ which is enhanced in comparison to its Langevin value χL by a factor of 2〈n〉.


1988 ◽  
Vol 66 (4) ◽  
pp. 718-724 ◽  
Author(s):  
Ruth Margaret Barron ◽  
Thomas Hugh Kenneth Barron ◽  
Paul Malcolm Mummery ◽  
Michael Sharkey

With typical pair potentials, a bond is stretched by vibrations along the bond directions, while contraction is caused by the tension set up by vibrations normal to the bond direction. The rôle of these two effects is studied in calculations for parallel linear-chain and zigzag-chain models. For linear chains and rigid zigzag chains, expansion is positive in the plane normal to the chain direction, although it may be strongly anisotropic in this plane. Expansion along the chain direction is negative, and typically an order of magnitude less than that normal to the chain. For a flexible zigzag chain with bond angle 90°, expansion is positive in all directions; the Grüneisen tensor is approximately isotropic, but elastic anisotropy leads to smaller expansion coefficients in the molecular planes. The Reuss-averaged Grüneisen function derived from (6–12) pair potentials is about 3.5 for most of the models; this is higher than observed experimentally in polycrystalline polyethylene, indicating the need for more realistic models of organic polymers.


Symmetry ◽  
2021 ◽  
Vol 13 (9) ◽  
pp. 1751
Author(s):  
Alireza Mashaghi ◽  
Roland van der Veen

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.


Author(s):  
Ago OMERBASIC ◽  

In this paper, we try to modestly, but strictly, using a mathematical approach, show that life was created with a certain goal and that the possibility of accidental origin of life is equal to zero. To calculate the probability of accidental creation of only one protein molecule, the basic building block of living systems, we selected a hemoglobin molecule that, because it is well studied, has become the standard for protein research. For comparison, together with this calculation, we also made a calculation of the probability of the systematic stacking of chaotically scattered playing cards from a certain height on a certain surface, a probability that is generally accepted as - improbably!


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