scholarly journals Maximal homology alignment: A new method based on two-dimensional homology

2019 ◽  
Author(s):  
Al Erives
Keyword(s):  
Sequence Alignment ◽  
Current Method ◽  
Two Dimensions ◽  
Nucleotide Position ◽  
Two Dimensional ◽  
Replication Slippage ◽  
Biologically Relevant ◽  
Dna Sequence Alignment ◽  
Gapped Alignment ◽  
Binary State

ABSTRACTMaximal homology alignment is a new biologically-relevant approach to DNA sequence alignment that maps the internal dispersed microhomology of individual sequences onto two dimensions. It departs from the current method of gapped alignment, which uses a simplified binary state model of nucleotide position. In gapped alignment nucleotide positions have either no relationship (1-to-None) or else orthological relationship (1-to-1) with nucleotides in other sequences. Maximal homology alignment, however, allows additional states such as 1-to-Many and Many-to-Many, thus modeling both orthological and paralogical relationships, which together comprise the main homology types. Maximal homology alignment collects dispersed microparalogy into the same alignment columns on multiple rows, and thereby generates a two-dimensional representation of a single sequence. Sequence alignment then proceeds as the alignment of two-dimensional topological objects. The operations of producing and aligning two-dimensional auto-alignments motivate a need for tests of two-dimensional homological integrity. Here, I work out and implement basic principles for computationally testing the two dimensions of positional homology, which are inherent to biological sequences due to replication slippage and related errors. I then show that maximal homology alignment is more informative than gapped alignment in modeling the evolution of genetic sequences. In general, MHA is more suited when small insertions and deletions predominantly originate as local microparalogy. These results show that both conserved and non-conserved genomic sequences are enriched with a signature of replication slippage relative to their random permutations.

Urbanicity, City Delegations, and Two-Dimensional Liberalism

2018 ◽  
Author(s):  
Thomas K. Ogorzalek
Keyword(s):  
National Level ◽  
Two Dimensions ◽  
Political Order ◽  
Two Dimensional ◽  
Local Institutions ◽  
Horizontal Integration ◽  
National Politics ◽  
United Front ◽  
Strategies For Success

This theoretical chapter develops the argument that the conditions of cities—large, densely populated, heterogeneous communities—generate distinctive governance demands supporting (1) market interventions and (2) group pluralism. Together, these positions constitute the two dimensions of progressive liberalism. Because of the nature of federalism, such policies are often best pursued at higher levels of government, which means that cities must present a united front in support of city-friendly politics. Such unity is far from assured on the national level, however, because of deep divisions between and within cities that undermine cohesive representation. Strategies for success are enhanced by local institutions of horizontal integration developed to address the governance demands of urbanicity, the effects of which are felt both locally and nationally in the development of cohesive city delegations and a unified urban political order capable of contending with other interests and geographical constituencies in national politics.

scholarly journals Interface Roughening in Two Dimensions

2021 ◽  
Vol 182 (3) ◽  
Author(s):  
Gernot Münster ◽  
Manuel Cañizares Guerrero
Keyword(s):  
Field Theory ◽  
Monte Carlo ◽  
Capillary Wave ◽  
System Size ◽  
Two Dimensions ◽  
Two Dimensional ◽  
Wave Approximation ◽  
Statistical Field ◽  
Statistical Field Theory ◽  
Interface Roughening

AbstractRoughening of interfaces implies the divergence of the interface width w with the system size L. For two-dimensional systems the divergence of $$w^2$$ w 2 is linear in L. In the framework of a detailed capillary wave approximation and of statistical field theory we derive an expression for the asymptotic behaviour of $$w^2$$ w 2 , which differs from results in the literature. It is confirmed by Monte Carlo simulations.

scholarly journals Is contact angle a cause or an effect? – A cautionary tale

2020 ◽  
Vol 146 ◽  
pp. 03004
Author(s):  
Douglas Ruth
Keyword(s):  
Contact Angle ◽  
Solid Surface ◽  
Contact Angles ◽  
Two Dimensions ◽  
Experimental Results ◽  
Flow In Porous Media ◽  
Two Dimensional ◽  
Wide Range ◽  
Fluid Drop ◽  
Surrounding Fluid

The most influential parameter on the behavior of two-component flow in porous media is “wettability”. When wettability is being characterized, the most frequently used parameter is the “contact angle”. When a fluid-drop is placed on a solid surface, in the presence of a second, surrounding fluid, the fluid-fluid surface contacts the solid-surface at an angle that is typically measured through the fluid-drop. If this angle is less than 90°, the fluid in the drop is said to “wet” the surface. If this angle is greater than 90°, the surrounding fluid is said to “wet” the surface. This definition is universally accepted and appears to be scientifically justifiable, at least for a static situation where the solid surface is horizontal. Recently, this concept has been extended to characterize wettability in non-static situations using high-resolution, two-dimensional digital images of multi-component systems. Using simple thought experiments and published experimental results, many of them decades old, it will be demonstrated that contact angles are not primary parameters – their values depend on many other parameters. Using these arguments, it will be demonstrated that contact angles are not the cause of wettability behavior but the effect of wettability behavior and other parameters. The result of this is that the contact angle cannot be used as a primary indicator of wettability except in very restricted situations. Furthermore, it will be demonstrated that even for the simple case of a capillary interface in a vertical tube, attempting to use simply a two-dimensional image to determine the contact angle can result in a wide range of measured values. This observation is consistent with some published experimental results. It follows that contact angles measured in two-dimensions cannot be trusted to provide accurate values and these values should not be used to characterize the wettability of the system.

scholarly journals Calderón problem for Maxwell's equations in two dimensions

2016 ◽  
Vol 24 (3) ◽  
Author(s):  
Oleg Y. Imanuvilov ◽  
Masahiro Yamamoto
Keyword(s):  
Maxwell’S Equations ◽  
Maxwell Equations ◽  
Maxwell's Equations ◽  
Two Dimensions ◽  
Two Dimensional ◽  
Global Uniqueness ◽  
Calderón Problem ◽  
Dirichlet To Neumann Map

AbstractWe prove the global uniqueness in determination of the conductivity, the permeability and the permittivity of the two-dimensional Maxwell equations by the partial Dirichlet-to-Neumann map limited to an arbitrary subboundary.

Estimates of critical percolation probabilities for a set of two-dimensional lattices

1972 ◽  
Vol 71 (1) ◽  
pp. 97-106 ◽  
Author(s):  
D. G. Neal
Keyword(s):  
Monte Carlo ◽  
Two Dimensions ◽  
Two Dimensional ◽  
Critical Percolation ◽  
Site Percolation

AbstractThis paper describes new detailed Monte Carlo investigations into bond and site percolation problems on the set of eleven regular and semi-regular (Archimedean) lattices in two dimensions.

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