scholarly journals PCPATCH

2021 ◽  
Vol 47 (3) ◽  
pp. 1-22
Author(s):  
Patrick E. Farrell ◽  
Matthew G. Knepley ◽  
Lawrence Mitchell ◽  
Florian Wechsung
Keyword(s):  
Saddle Point ◽  
Degrees Of Freedom ◽  
Rapid Development ◽  
Construction Rule ◽  
Relaxation Methods ◽  
Fast Solvers ◽  
Multigrid Convergence ◽  
Wide Range ◽  
Topological Construction

Effective relaxation methods are necessary for good multigrid convergence. For many equations, standard Jacobi and Gauß–Seidel are inadequate, and more sophisticated space decompositions are required; examples include problems with semidefinite terms or saddle point structure. In this article, we present a unifying software abstraction, PCPATCH, for the topological construction of space decompositions for multigrid relaxation methods. Space decompositions are specified by collecting topological entities in a mesh (such as all vertices or faces) and applying a construction rule (such as taking all degrees of freedom in the cells around each entity). The software is implemented in PETSc and facilitates the elegant expression of a wide range of schemes merely by varying solver options at runtime. In turn, this allows for the very rapid development of fast solvers for difficult problems.

Understanding Conformational Entropy in Small Molecules

2020 ◽  
Author(s):  
Lucian Chan ◽  
Garrett Morris ◽  
Geoffrey Hutchison
Keyword(s):  
Small Molecules ◽  
Degrees Of Freedom ◽  
Absolute Error ◽  
Low Energy ◽  
Standard Entropy ◽  
Free Energies ◽  
Conformational Entropy ◽  
Wide Range ◽  
High Degree ◽  
Empirical Corrections

The calculation of the entropy of flexible molecules can be challenging, since the number of possible conformers grows exponentially with molecule size and many low-energy conformers may be thermally accessible. Different methods have been proposed to approximate the contribution of conformational entropy to the molecular standard entropy, including performing thermochemistry calculations with all possible stable conformations, and developing empirical corrections from experimental data. We have performed conformer sampling on over 120,000 small molecules generating some 12 million conformers, to develop models to predict conformational entropy across a wide range of molecules. Using insight into the nature of conformational disorder, our cross-validated physically-motivated statistical model can outperform common machine learning and deep learning methods, with a mean absolute error ≈4.8 J/mol•K, or under 0.4 kcal/mol at 300 K. Beyond predicting molecular entropies and free energies, the model implies a high degree of correlation between torsions in most molecules, often as- sumed to be independent. While individual dihedral rotations may have low energetic barriers, the shape and chemical functionality of most molecules necessarily correlate their torsional degrees of freedom, and hence restrict the number of low-energy conformations immensely. Our simple models capture these correlations, and advance our understanding of small molecule conformational entropy.

scholarly journals Quantum information probes of charge fractionalization in large-N gauge theories

2021 ◽  
Vol 2021 (5) ◽  
Author(s):  
Brandon S. DiNunno ◽  
Niko Jokela ◽  
Juan F. Pedraza ◽  
Arttu Pönni
Keyword(s):  
Degrees Of Freedom ◽  
Gauge Theories ◽  
Entanglement Entropy ◽  
Coarse Grained ◽  
Strongly Coupled ◽  
Information Theoretic ◽  
Large N ◽  
Wide Range ◽  
Charge Fractionalization ◽  
Electric Flux

Abstract We study in detail various information theoretic quantities with the intent of distinguishing between different charged sectors in fractionalized states of large-N gauge theories. For concreteness, we focus on a simple holographic (2 + 1)-dimensional strongly coupled electron fluid whose charged states organize themselves into fractionalized and coherent patterns at sufficiently low temperatures. However, we expect that our results are quite generic and applicable to a wide range of systems, including non-holographic. The probes we consider include the entanglement entropy, mutual information, entanglement of purification and the butterfly velocity. The latter turns out to be particularly useful, given the universal connection between momentum and charge diffusion in the vicinity of a black hole horizon. The RT surfaces used to compute the above quantities, though, are largely insensitive to the electric flux in the bulk. To address this deficiency, we propose a generalized entanglement functional that is motivated through the Iyer-Wald formalism, applied to a gravity theory coupled to a U(1) gauge field. We argue that this functional gives rise to a coarse grained measure of entanglement in the boundary theory which is obtained by tracing over (part) of the fractionalized and cohesive charge degrees of freedom. Based on the above, we construct a candidate for an entropic c-function that accounts for the existence of bulk charges. We explore some of its general properties and their significance, and discuss how it can be used to efficiently account for charged degrees of freedom across different energy scales.

scholarly journals Analysis of Dynamic Response of a Two Degrees of Freedom (2-DOF) Ball Bearing Nonlinear Model

2021 ◽  
Vol 11 (2) ◽  
pp. 787
Author(s):  
Bartłomiej Ambrożkiewicz ◽  
Grzegorz Litak ◽  
Anthimos Georgiadis ◽  
Nicolas Meier ◽  
Alexander Gassner
Keyword(s):  
Mathematical Model ◽  
Degrees Of Freedom ◽  
Ball Bearing ◽  
Hertzian Contact ◽  
Two Degrees Of Freedom ◽  
Wide Range ◽  
Shape Errors ◽  
Nonlinear Features ◽  
Fourier Transform Phase ◽  
Hertzian Contact Theory

Often the input values used in mathematical models for rolling bearings are in a wide range, i.e., very small values of deformation and damping are confronted with big values of stiffness in the governing equations, which leads to miscalculations. This paper presents a two degrees of freedom (2-DOF) dimensionless mathematical model for ball bearings describing a procedure, which helps to scale the problem and reveal the relationships between dimensionless terms and their influence on the system’s response. The derived mathematical model considers nonlinear features as stiffness, damping, and radial internal clearance referring to the Hertzian contact theory. Further, important features are also taken into account including an external load, the eccentricity of the shaft-bearing system, and shape errors on the raceway investigating variable dynamics of the ball bearing. Analysis of obtained responses with Fast Fourier Transform, phase plots, orbit plots, and recurrences provide a rich source of information about the dynamics of the system and it helped to find the transition between the periodic and chaotic response and how it affects the topology of RPs and recurrence quantificators.

scholarly journals Advanced Functional Materials Based on Nanocellulose for Pharmaceutical/Medical Applications

Pharmaceutics ◽  
2021 ◽  
Vol 13 (8) ◽  
pp. 1125
Author(s):  
Raluca Nicu ◽  
Florin Ciolacu ◽  
Diana E. Ciolacu
Keyword(s):  
Rapid Development ◽  
Cellulose Nanofibrils ◽  
Functional Materials ◽  
Medical Applications ◽  
Bacterial Nanocellulose ◽  
Green Materials ◽  
Wide Range ◽  
In Vivo Cytotoxicity

Nanocelluloses (NCs), with their remarkable characteristics, have proven to be one of the most promising “green” materials of our times and have received special attention from researchers in nanomaterials. A diversity of new functional materials with a wide range of biomedical applications has been designed based on the most desirable properties of NCs, such as biocompatibility, biodegradability, and their special physicochemical properties. In this context and under the pressure of rapid development of this field, it is imperative to synthesize the successes and the new requirements in a comprehensive review. The first part of this work provides a brief review of the characteristics of the NCs (cellulose nanocrystals—CNC, cellulose nanofibrils—CNF, and bacterial nanocellulose—BNC), as well as of the main functional materials based on NCs (hydrogels, nanogels, and nanocomposites). The second part presents an extensive review of research over the past five years on promising pharmaceutical and medical applications of nanocellulose-based materials, which have been discussed in three important areas: drug-delivery systems, materials for wound-healing applications, as well as tissue engineering. Finally, an in-depth assessment of the in vitro and in vivo cytotoxicity of NCs-based materials, as well as the challenges related to their biodegradability, is performed.

scholarly journals Single and Double Infections with Wolbachia in the Parasitic Wasp Nasonia vitripennis Effects on Compatibility

Genetics ◽  
1996 ◽  
Vol 143 (2) ◽  
pp. 961-972 ◽  
Author(s):  
Marie-Jeanne Perrot-Minnot ◽  
Li Rong Guo ◽  
John H Werren
Keyword(s):  
Genomic Dna ◽  
Rapid Development ◽  
Parasitic Wasp ◽  
Pcr Amplification ◽  
Bacterial Strains ◽  
Nasonia Vitripennis ◽  
Larval Diapause ◽  
Wide Range ◽  
Reproductive Incompatibility ◽  
Infected Line

Abstract Wolbachia are cytoplasmically inherited bacteria responsible for reproductive incompatibility in a wide range of insects. There has been little exploration, however, of within species Wolbachia polymorphisms and their effects on compatibility. Here we show that some strains of the parasitic wasp Nasonia vitripennis are infected with two distinct bacterial strains (A and B) whereas others are singly infected (A or B). Double and single infections are confirmed by both PCR amplification and Southern analysis of genomic DNA. Furthermore, it is shown that prolonged larval diapause (the overwintering stage of the wasp) of a double-infected strain can lead to stochastic loss of one or both bacterial strains. After diapause of a double-infected line, sublines were produced with AB, A only, B only or no Wolbachia. A and B sublines are bidirectionally incompatible, whereas males from AB lines are unidirectionally incompatible with females of A and B sublines. Results therefore show rapid development of bidirectional incompatibility within a species due to segregation of associated symbiotic bacteria.

Estimation of the Thermodynamic Properties of Branched Hydrocarbons

2000 ◽  
Vol 122 (3) ◽  
pp. 147-152 ◽  
Author(s):  
Hui He ◽  
Mohamad Metghalchi ◽  
James C. Keck
Keyword(s):  
Thermodynamic Properties ◽  
Degrees Of Freedom ◽  
Statistical Thermodynamic ◽  
Motion Modes ◽  
Branched Alkanes ◽  
Branched Hydrocarbons ◽  
Wide Range ◽  
On Line ◽  
Kinetic Calculations ◽  
Good Agreement

A simple model has been developed to estimate the sensible thermodynamic properties such as Gibbs free energy, enthalpy, heat capacity, and entropy of hydrocarbons over a wide range of temperatures with special attention to the branched molecules. The model is based on statistical thermodynamic expressions incorporating translational, rotational and vibrational motions of the atoms. A method to determine the number of degrees of freedom for different motion modes (bending and torsion) has been established. Branched rotational groups, such as CH3 and OH, have been considered. A modification of the characteristic temperatures for different motion mode has been made which improves the agreement with the exact values for simple cases. The properties of branched alkanes up to 2,3,4,-trimthylpentane have been calculated and the results are in good agreement with the experimental data. A relatively small number of parameters are needed in this model to estimate the sensible thermodynamic properties of a wide range of species. The model may also be used to estimate the properties of molecules and their isomers, which have not been measured, and is simple enough to be easily programmed as a subroutine for on-line kinetic calculations. [S0195-0738(00)00902-X]

scholarly journals Multi-stable composite twisting structure for morphing applications

2012 ◽  
Vol 468 (2141) ◽  
pp. 1230-1251 ◽  
Author(s):  
X. Lachenal ◽  
P. M. Weaver ◽  
S. Daynes
Keyword(s):  
Analytical Model ◽  
Material Properties ◽  
Degrees Of Freedom ◽  
Design Parameters ◽  
Engineering Structures ◽  
The Past ◽  
Wide Range ◽  
Morphing Structure ◽  
Low Mass ◽  
Unstable States

Conventional shape-changing engineering structures use discrete parts articulated around a number of linkages. Each part carries the loads, and the articulations provide the degrees of freedom of the system, leading to heavy and complex mechanisms. Consequently, there has been increased interest in morphing structures over the past decade owing to their potential to combine the conflicting requirements of strength, flexibility and low mass. This article presents a novel type of morphing structure capable of large deformations, simply consisting of two pre-stressed flanges joined to introduce two stable configurations. The bistability is analysed through a simple analytical model, predicting the positions of the stable and unstable states for different design parameters and material properties. Good correlation is found between experimental results, finite-element modelling and predictions from the analytical model for one particular example. A wide range of design parameters and material properties is also analytically investigated, yielding a remarkable structure with zero stiffness along the twisting axis.

ORGANIZATION OF ROAD TRAFFIC TAKING INTO ACCOUNT ELECTRIC ROUTE PASSENGER TRANSPORT

2021 ◽  
Vol 2 (65) ◽  
pp. 66-77
Author(s):  
Denis V. Kapsky ◽  
◽  
Sergey S. Semchenkov ◽  
Evgeny N. Kot ◽  
◽  
...  
Keyword(s):  
Traffic Management ◽  
Road Traffic ◽  
Rapid Development ◽  
Living Environment ◽  
Transport Sector ◽  
Passenger Transport ◽  
Wide Range ◽  
Practical Development ◽  
The Republic ◽  
Conducting Research

The rapid development of the transport sector leads not only to positive changes in the life of cities and towns, to an increase in convenience and comfort for residents, but also worsens the ecology and their living environment. The “profitable-safe” dilemma can be solved by the approach of environmentally oriented selection of the type of route passenger transport and decisionmaking in favor of electric route passenger transport. The article discusses the types of such transport on the example of the experience of their use in the Republic of Belarus. The classification and systematization developed by the authors are presented with subsequent recommendations for its application. On the basis of the results of the authors’ research, the issues of interaction of rail and non-rail route vehicles with an electric drive with the organization of road traffic are separately considered. The presented materials can be useful to a wide range of readers, as well as to specialists conducting research and practical development in the field of electrically powered route vehicles and traffic management.

scholarly journals Protein dynamics revealed by NMR relaxation methods

2018 ◽  
Vol 2 (1) ◽  
pp. 93-105 ◽  
Author(s):  
Fa-An Chao ◽  
R. Andrew Byrd
Keyword(s):  
Protein Dynamics ◽  
Structural Biology ◽  
Dynamic Models ◽  
Dimensional Space ◽  
Three Dimensional ◽  
Data Bank ◽  
Biological Macromolecules ◽  
Relaxation Methods ◽  
Genomic Databases ◽  
Wide Range

Structural biology often focuses primarily on three-dimensional structures of biological macromolecules, deposited in the Protein Data Bank (PDB). This resource is a remarkable entity for the worldwide scientific and medical communities, as well as the general public, as it is a growing translation into three-dimensional space of the vast information in genomic databases, e.g. GENBANK. There is, however, significantly more to understanding biological function than the three-dimensional co-ordinate space for ground-state structures of biomolecules. The vast array of biomolecules experiences natural dynamics, interconversion between multiple conformational states, and molecular recognition and allosteric events that play out on timescales ranging from picoseconds to seconds. This wide range of timescales demands ingenious and sophisticated experimental tools to sample and interpret these motions, thus enabling clearer insights into functional annotation of the PDB. NMR spectroscopy is unique in its ability to sample this range of timescales at atomic resolution and in physiologically relevant conditions using spin relaxation methods. The field is constantly expanding to provide new creative experiments, to yield more detailed coverage of timescales, and to broaden the power of interpretation and analysis methods. This review highlights the current state of the methodology and examines the extension of analysis tools for more complex experiments and dynamic models. The future for understanding protein dynamics is bright, and these extended tools bring greater compatibility with developments in computational molecular dynamics, all of which will further our understanding of biological molecular functions. These facets place NMR as a key component in integrated structural biology.

scholarly journals Culinary and Medicinal Mushrooms: Insight into Growing Technologies

2021 ◽  
Vol 55 (2) ◽  
Author(s):  
Piotr Zięba ◽  
Agnieszka Sękara ◽  
Katarzyna Sułkowska-Ziaja ◽  
Bożena Muszyńska
Keyword(s):  
Rapid Development ◽  
Essential Elements ◽  
Market Demand ◽  
Fruiting Bodies ◽  
Mushroom Species ◽  
Medicinal Mushrooms ◽  
Wide Range ◽  
Growing Conditions ◽  
Natural Medicines ◽  
Modern Technologies

Humans have used mushrooms from the beginning of their history. However, during the last few decades, the market demand for these fruiting bodies has increased significantly owing to the spread in the capabilities of culinary and pharmacological exploitation. Natural mushroom resources have become insufficient to meet the support needs. Therefore, traditional methods of extensive cultivation as well as modern technologies have been exploited to develop effective growing recommendations for dozens of economically important mushroom species. Mushrooms can decompose a wide range of organic materials, including organic waste. They play a fundamental role in nutrient cycling and exchange in the environment. The challenge is a proper substrate composition, including bio-fortified essential elements, and the application of growing conditions to enable a continuous supply of fruiting bodies of market quality and stabilized chemical composition. Many mushroom species are used for food preparation. Moreover, they are treated as functional foods, because they have health benefits beyond their nutritional value, and are used as natural medicines in many countries. Owing to the rapid development of mushroom farming, we reviewed the growing technologies used worldwide for mushroom species developed for food, processing, and pharmacological industries.

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