scholarly journals Unified treatment of synchronization patterns in generalized networks with higher-order, multilayer, and temporal interactions

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Yuanzhao Zhang ◽  
Vito Latora ◽  
Adilson E. Motter
Keyword(s):  
Higher Order ◽  
Cluster Synchronization ◽  
Block Diagonalization ◽  
Unified Framework ◽  
Emergent Phenomena ◽  
Wide Range ◽  
Generalized Networks ◽  
The Stability ◽  
Temporal Interactions ◽  
Synchronization Pattern

AbstractWhen describing complex interconnected systems, one often has to go beyond the standard network description to account for generalized interactions. Here, we establish a unified framework to simplify the stability analysis of cluster synchronization patterns for a wide range of generalized networks, including hypergraphs, multilayer networks, and temporal networks. The framework is based on finding a simultaneous block diagonalization of the matrices encoding the synchronization pattern and the network topology. As an application, we use simultaneous block diagonalization to unveil an intriguing type of chimera states that appear only in the presence of higher-order interactions. The unified framework established here can be extended to other dynamical processes and can facilitate the discovery of emergent phenomena in complex systems with generalized interactions.

Performance of Electronic Structure Methods for the Description of Hückel-Möbius Interconversions in Extended π-Systems

2019 ◽  
Author(s):  
Tatiana Woller ◽  
Ambar Banerjee ◽  
Nitai Sylvetsky ◽  
Xavier Deraet ◽  
Frank De Proft ◽  
...  
Keyword(s):  
Electronic Structure ◽  
Basis Set ◽  
Dft Methods ◽  
Molecular Switching ◽  
Wide Range ◽  
Electronic Structure Methods ◽  
Explicitly Correlated ◽  
Relative Errors ◽  
The Stability ◽  
Basis Set Expansion

<p>Expanded porphyrins provide a versatile route to molecular switching devices due to their ability to shift between several π-conjugation topologies encoding distinct properties. Taking into account its size and huge conformational flexibility, DFT remains the workhorse for modeling such extended macrocycles. Nevertheless, the stability of Hückel and Möbius conformers depends on a complex interplay of different factors, such as hydrogen bonding, p···p stacking, steric effects, ring strain and electron delocalization. As a consequence, the selection of an exchange-correlation functional for describing the energy profile of topological switches is very difficult. For these reasons, we have examined the performance of a variety of wavefunction methods and density functionals for describing the thermochemistry and kinetics of topology interconversions across a wide range of macrocycles. Especially for hexa- and heptaphyrins, the Möbius structures have a pronouncedly stronger degree of static correlation than the Hückel and figure-eight structures, and as a result the relative energies of singly-twisted structures are a challenging test for electronic structure methods. Comparison of limited orbital space full CI calculations with CCSD(T) calculations within the same active spaces shows that post-CCSD(T) correlation contributions to relative energies are very minor. At the same time, relative energies are weakly sensitive to further basis set expansion, as proven by the minor energy differences between MP2/cc-pVDZ and explicitly correlated MP2-F12/cc-pVDZ-F12 calculations. Hence, our CCSD(T) reference values are reasonably well-converged in both 1-particle and n-particle spaces. While conventional MP2 and MP3 yield very poor results, SCS-MP2 and particularly SOS-MP2 and SCS-MP3 agree to better than 1 kcal mol<sup>-1</sup> with the CCSD(T) relative energies. Regarding DFT methods, only M06-2X provides relative errors close to chemical accuracy with a RMSD of 1.2 kcal mol<sup>-1</sup>. While the original DSD-PBEP86 double hybrid performs fairly poorly for these extended p-systems, the errors drop down to 2 kcal mol<sup>-1</sup> for the revised revDSD-PBEP86-NL, again showing that same-spin MP2-like correlation has a detrimental impact on performance like the SOS-MP2 results. </p>

Current Trends in Biotherapeutic Higher Order Structure Characterization by Irreversible Covalent Footprinting Mass Spectrometry

2019 ◽  
Vol 26 (1) ◽  
pp. 35-43 ◽  
Author(s):  
Natalie K. Garcia ◽  
Galahad Deperalta ◽  
Aaron T. Wecksler
Keyword(s):  
Mass Spectrometry ◽  
Protein Structure ◽  
Protein Interactions ◽  
Quaternary Structure ◽  
Solvent Accessibility ◽  
Higher Order ◽  
Structure Characterization ◽  
Order Structure ◽  
Protein Footprinting ◽  
Wide Range

Background: Biotherapeutics, particularly monoclonal antibodies (mAbs), are a maturing class of drugs capable of treating a wide range of diseases. Therapeutic function and solutionstability are linked to the proper three-dimensional organization of the primary sequence into Higher Order Structure (HOS) as well as the timescales of protein motions (dynamics). Methods that directly monitor protein HOS and dynamics are important for mapping therapeutically relevant protein-protein interactions and assessing properly folded structures. Irreversible covalent protein footprinting Mass Spectrometry (MS) tools, such as site-specific amino acid labeling and hydroxyl radical footprinting are analytical techniques capable of monitoring the side chain solvent accessibility influenced by tertiary and quaternary structure. Here we discuss the methodology, examples of biotherapeutic applications, and the future directions of irreversible covalent protein footprinting MS in biotherapeutic research and development. Conclusion: Bottom-up mass spectrometry using irreversible labeling techniques provide valuable information for characterizing solution-phase protein structure. Examples range from epitope mapping and protein-ligand interactions, to probing challenging structures of membrane proteins. By paring these techniques with hydrogen-deuterium exchange, spectroscopic analysis, or static-phase structural data such as crystallography or electron microscopy, a comprehensive understanding of protein structure can be obtained.

Insights into Potent Therapeutical Antileukemic Agent L-glutaminase Enzyme Under Solid-state Fermentation: A Review

2020 ◽  
Vol 21 (3) ◽  
pp. 211-220 ◽  
Author(s):  
Chandrasai Potla Durthi ◽  
Madhuri Pola ◽  
Satish Babu Rajulapati ◽  
Anand Kishore Kola
Keyword(s):  
Solid State ◽  
Solid State Fermentation ◽  
Food Industry ◽  
Energy Requirement ◽  
Production Studies ◽  
Wide Range ◽  
Hybridoma Technology ◽  
Bacteria And Fungi ◽  
The Stability ◽  
Glutaminase Activity

Aim & objective: To review the applications and production studies of reported antileukemic drug L-glutaminase under Solid-state Fermentation (SSF). Overview: An amidohydrolase that gained economic importance because of its wide range of applications in the pharmaceutical industry, as well as the food industry, is L-glutaminase. The medical applications utilized it as an anti-tumor agent as well as an antiretroviral agent. L-glutaminase is employed in the food industry as an acrylamide degradation agent, as a flavor enhancer and for the synthesis of theanine. Another application includes its use in hybridoma technology as a biosensing agent. Because of its diverse applications, scientists are now focusing on enhancing the production and optimization of L-glutaminase from various sources by both Solid-state Fermentation (SSF) and submerged fermentation studies. Of both types of fermentation processes, SSF has gained importance because of its minimal cost and energy requirement. L-glutaminase can be produced by SSF from both bacteria and fungi. Single-factor studies, as well as multi-level optimization studies, were employed to enhance L-glutaminase production. It was concluded that L-glutaminase activity achieved by SSF was 1690 U/g using wheat bran and Bengal gram husk by applying feed-forward artificial neural network and genetic algorithm. The highest L-glutaminase activity achieved under SSF was 3300 U/gds from Bacillus sp., by mixture design. Purification and kinetics studies were also reported to find the molecular weight as well as the stability of L-glutaminase. Conclusion: The current review is focused on the production of L-glutaminase by SSF from both bacteria and fungi. It was concluded from reported literature that optimization studies enhanced L-glutaminase production. Researchers have also confirmed antileukemic and anti-tumor properties of the purified L-glutaminase on various cell lines.

scholarly journals Polymer-Drug Conjugates as Nanotheranostic Agents

2021 ◽  
Vol 2 (1) ◽  
pp. 63-81
Author(s):  
Sajana Manandhar ◽  
Erica Sjöholm ◽  
Johan Bobacka ◽  
Jessica M. Rosenholm ◽  
Kuldeep K. Bansal
Keyword(s):  
Drug Delivery ◽  
Drug Release ◽  
Treatment Options ◽  
The Body ◽  
Drug Conjugates ◽  
Imaging Characteristics ◽  
Wide Range ◽  
Systemic Side Effects ◽  
Theranostic Agents ◽  
The Stability

Since the last decade, the polymer-drug conjugate (PDC) approach has emerged as one of the most promising drug-delivery technologies owing to several benefits like circumventing premature drug release, offering controlled and targeted drug delivery, improving the stability, safety, and kinetics of conjugated drugs, and so forth. In recent years, PDC technology has advanced with the objective to further enhance the treatment outcomes by integrating nanotechnology and multifunctional characteristics into these systems. One such development is the ability of PDCs to act as theranostic agents, permitting simultaneous diagnosis and treatment options. Theranostic nanocarriers offer the opportunity to track the distribution of PDCs within the body and help to localize the diseased site. This characteristic is of particular interest, especially among those therapeutic approaches where external stimuli are supposed to be applied for abrupt drug release at the target site for localized delivery to avoid systemic side effects (e.g., Visudyne®). Thus, with the help of this review article, we are presenting the most recent updates in the domain of PDCs as nanotheranostic agents. Different methodologies utilized to design PDCs along with imaging characteristics and their applicability in a wide range of diseases, have been summarized in this article.

scholarly journals Emergent chiral symmetry in a three-dimensional interacting Dirac liquid

2021 ◽  
Vol 2021 (1) ◽  
Author(s):  
András L. Szabó ◽  
Bitan Roy
Keyword(s):  
Fixed Points ◽  
Chiral Symmetry ◽  
Rotational Symmetry ◽  
Three Dimensional ◽  
Spatial Dimension ◽  
Dirac Fermions ◽  
Electronic Interactions ◽  
Emergent Phenomena ◽  
Ordered Phases ◽  
The Stability

Abstract We compute the effects of strong Hubbardlike local electronic interactions on three-dimensional four-component massless Dirac fermions, which in a noninteracting system possess a microscopic global U(1) ⊗ SU(2) chiral symmetry. A concrete lattice realization of such chiral Dirac excitations is presented, and the role of electron-electron interactions is studied by performing a field theoretic renormalization group (RG) analysis, controlled by a small parameter ϵ with ϵ = d−1, about the lower-critical one spatial dimension. Besides the noninteracting Gaussian fixed point, the system supports four quantum critical and four bicritical points at nonvanishing interaction couplings ∼ ϵ. Even though the chiral symmetry is absent in the interacting model, it gets restored (either partially or fully) at various RG fixed points as emergent phenomena. A representative cut of the global phase diagram displays a confluence of scalar and pseudoscalar excitonic and superconducting (such as the s-wave and p-wave) mass ordered phases, manifesting restoration of (a) chiral U(1) symmetry between two excitonic masses for repulsive interactions and (b) pseudospin SU(2) symmetry between scalar or pseudoscalar excitonic and superconducting masses for attractive interactions. Finally, we perturbatively study the effects of weak rotational symmetry breaking on the stability of various RG fixed points.

scholarly journals No-z Model for Magnetic Fields of Different Astrophysical Objects and Stability of the Solutions

Data ◽  
2021 ◽  
Vol 6 (1) ◽  
pp. 4
Author(s):  
Evgeny Mikhailov ◽  
Daniela Boneva ◽  
Maria Pashentseva
Keyword(s):  
Magnetic Field ◽  
Magnetic Fields ◽  
Large Scale ◽  
Point Of View ◽  
Accretion Discs ◽  
Wide Range ◽  
Astrophysical Objects ◽  
Alpha Effect ◽  
The Stability ◽  
The Magnetic Field

A wide range of astrophysical objects, such as the Sun, galaxies, stars, planets, accretion discs etc., have large-scale magnetic fields. Their generation is often based on the dynamo mechanism, which is connected with joint action of the alpha-effect and differential rotation. They compete with the turbulent diffusion. If the dynamo is intensive enough, the magnetic field grows, else it decays. The magnetic field evolution is described by Steenbeck—Krause—Raedler equations, which are quite difficult to be solved. So, for different objects, specific two-dimensional models are used. As for thin discs (this shape corresponds to galaxies and accretion discs), usually, no-z approximation is used. Some of the partial derivatives are changed by the algebraic expressions, and the solenoidality condition is taken into account as well. The field generation is restricted by the equipartition value and saturates if the field becomes comparable with it. From the point of view of mathematical physics, they can be characterized as stable points of the equations. The field can come to these values monotonously or have oscillations. It depends on the type of the stability of these points, whether it is a node or focus. Here, we study the stability of such points and give examples for astrophysical applications.

scholarly journals Cycle and flow trusses in directed networks

2016 ◽  
Vol 3 (11) ◽  
pp. 160270 ◽  
Author(s):  
Taro Takaguchi ◽  
Yuichi Yoshida
Keyword(s):  
Truss Structures ◽  
Directed Network ◽  
Unified Framework ◽  
Directed Networks ◽  
Research Fields ◽  
Wide Range ◽  
Definition Of ◽  
Information Finding ◽  
Empirical Networks ◽  
Module Structures

When we represent real-world systems as networks, the directions of links often convey valuable information. Finding module structures that respect link directions is one of the most important tasks for analysing directed networks. Although many notions of a directed module have been proposed, no consensus has been reached. This lack of consensus results partly because there might exist distinct types of modules in a single directed network, whereas most previous studies focused on an independent criterion for modules. To address this issue, we propose a generic notion of the so-called truss structures in directed networks. Our definition of truss is able to extract two distinct types of trusses, named the cycle truss and the flow truss, from a unified framework. By applying the method for finding trusses to empirical networks obtained from a wide range of research fields, we find that most real networks contain both cycle and flow trusses. In addition, the abundance of (and the overlap between) the two types of trusses may be useful to characterize module structures in a wide variety of empirical networks. Our findings shed light on the importance of simultaneously considering different types of modules in directed networks.

A Parallel HOFD Scheme for Direct Numerical Simulation of Turbulent Magnetically Driven Flows

2001 ◽  
Author(s):  
X. Ai ◽  
B. Q. Li
Keyword(s):  
Numerical Simulation ◽  
Finite Difference ◽  
Direct Numerical Simulation ◽  
Turbulent Flows ◽  
Parallel Machines ◽  
Higher Order ◽  
Electrically Conducting ◽  
Wide Range ◽  
Order Scheme ◽  
Higher Order Scheme

Abstract Turbulent magnetically flows occur in a wide range of material processing systems involving electrically conducting melts. This paper presents a parallel higher order scheme for the direct numerical simulation of turbulent magnetically driven flows in induction channels. The numerical method is based on the higher order finite difference algorithm, which enjoys the spectral accuracy while minimizing the computational intensity. This, coupled with the parallel computing strategy, provides a very useful means to simulate turbulent flows. The higher order finite difference formulation of magnetically driven flow problems is described in this paper. The details of the parallel algorithm and its implementation for the simulations on parallel machines are discussed. The accuracy and numerical performance of the higher order finite difference scheme are assessed in comparison with the spectral method. The examples of turbulent magnetically driven flows in induction channels and pressure gradient driven flows in regular channels are given, and the computed results are compared with experimental measurements wherever possible.

Comparative study of finite element analysis of steel silos with rectangular and I stiffeners

2021 ◽  
Vol 10 (1) ◽  
pp. 9
Author(s):  
Prasad Lakshmi ◽  
Neethu Elsa Anil
Keyword(s):  
Reinforced Concrete ◽  
Element Analysis ◽  
Plate Structures ◽  
Steel Reinforced Concrete ◽  
Wide Range ◽  
Earthquake Load ◽  
The Stability ◽  
Dynamic Loading Conditions ◽  
Steel Silos ◽  
Static And Dynamic Loading

Silos are used by a wide range of industries to store bulk solids in quantities ranging from a few tones to hundreds or thousands of tones. They can be constructed of steel or reinforced concrete. Steel bins range from heavily stiffened flat plate structures to efficient unstiffened shell structures. They can be closed or open. They are subjected to many different static and dynamic loading conditions, mainly due to the unique characteristics of stored materials. Wind and earthquake load often undermine the stability of the silos. A steel silo with and without stiffeners is adopted and static structural analysis and dynamic analysis is done. The analysis is done by idealizing geometry, material and boundary conditions. Keywords: steel, reinforced concrete, silos.

Understanding Micro-Droplet Interface Bilayers for Developing Bioinspired Sensors

2013 ◽  
Author(s):  
Guru Venkatesan ◽  
Andy Sarles
Keyword(s):  
Water Droplet ◽  
Morphological Changes ◽  
High Surface ◽  
High Surface Area ◽  
Material System ◽  
Modes Of Operation ◽  
New Class ◽  
Wide Range ◽  
Droplet Sizes ◽  
The Stability

Droplet-based biomolecular arrays form the basis for a new class of bioinspired material system, whereby decreasing the sizes of the droplets and increasing the number of droplets can lead to higher functional density for the array. In this paper, we report on a non-microfluidic approach to form and connect nanoliter-to-femtoliter, lipid-coated aqueous droplets in oil to form micro-droplet interface bilayers (μDIBs). Two different modes of operation are reported for dispensing a wide range of droplet sizes (2–200μm radius). Due to the high surface-area-to-volume ratios of microdroplets at these length scales, droplet shrinking is prominent, which affects the stability and lifetime of the bilayer. To better quantify these effects, we measure the shrinkage rates for 8 different water droplet/oil compositions and study the effect of lipid placement and lipid type on morphological changes to μDIBs.

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