scholarly journals Modal Analysis of the Lysozyme Protein Considering All-Atom and Coarse-Grained Finite Element Models

2021 ◽  
Vol 11 (2) ◽  
pp. 547
Author(s):  
Gustavo Giordani ◽  
Domenico Scaramozzino ◽  
Ignacio Iturrioz ◽  
Giuseppe Lacidogna ◽  
Alberto Carpinteri
Keyword(s):  
Modal Analysis ◽  
Numerical Solutions ◽  
Dynamic Properties ◽  
Low Frequency ◽  
Coarse Grained ◽  
Representative Point ◽  
Dynamic Simulations ◽  
Quick Method ◽  
Egg White Lysozyme ◽  
General Terms

Proteins are the fundamental entities of several organic activities. They are essential for a broad range of tasks in a way that their shapes and folding processes are crucial to achieving proper biological functions. Low-frequency modes, generally associated with collective movements at terahertz (THz) and sub-terahertz frequencies, have been appointed as critical for the conformational processes of many proteins. Dynamic simulations, such as molecular dynamics, are vastly applied by biochemical researchers in this field. However, in the last years, proposals that define the protein as a simplified elastic macrostructure have shown appealing results when dealing with this type of problem. In this context, modal analysis based on different modelization techniques, i.e., considering both an all-atom (AA) and coarse-grained (CG) representation, is proposed to analyze the hen egg-white lysozyme. This work presents new considerations and conclusions compared to previous analyses. Experimental values for the B-factor, considering all the heavy atoms or only one representative point per amino acid, are used to evaluate the validity of the numerical solutions. In general terms, this comparison allows the assessment of the regional flexibility of the protein. Besides, the low computational requirements make this approach a quick method to extract the protein’s dynamic properties under scrutiny.

A Molecular Dynamics Study on the Static and Dynamic Properties of Lubricant PFPE in Hard Disk Driver

2005 ◽  
Author(s):  
Xin Li ◽  
Yuanzhong Hu ◽  
Hui Wang
Keyword(s):  
Dynamic Properties ◽  
Polymer Structure ◽  
Coarse Grained ◽  
Precursor Film ◽  
Static Properties ◽  
Dynamic Simulations ◽  
Atomic Diameter ◽  
Service Durability ◽  
Hard Disk Driver ◽  
The One

The static and dynamic properties of lubricant PFPE are important for the service durability and reliability of the computer head-disk device. Thus molecular dynamic simulations based on a coarse-grained, bead-spring model are adopted to study those properties. On the one hand, we investigate the static properties and infer the structure of both nonpolar and polar PFPE films. For a nonpolar PFPE film, there is a layering structure in the surface layer. And for a polar PFPE film, besides layering structure, there is a bi-polymer structure in the bulk layer. On the other hand, we investigate the dynamic properties and find that for nonpolar PFPE film, a precursor film around one atomic diameter thickness develops according to layering structure; while for polar PFPE film, besides a precursor film, a much steeper and slower spreading shape appears according to bi-polymer structure.

scholarly journals Influence of dynamic properties on scaffoldings safety

2021 ◽  
Vol 21 (4) ◽  
Author(s):  
Ewa Błazik-Borowa ◽  
Jarosław Bęc
Keyword(s):  
Natural Frequency ◽  
Dynamic Behavior ◽  
Natural Frequencies ◽  
Dynamic Properties ◽  
Low Frequency ◽  
Mode Shapes ◽  
Natural Mode ◽  
Longitudinal Vibrations ◽  
Dynamic Simulations ◽  
Dangerous Situation

AbstractScaffoldings are used for works at height and in places that are hard to reach, which makes such works dangerous to employees and accidents occur frequently. Loads generated by scaffolding users cannot be avoided. Moving workers excite low-frequency (1–2 Hz) vibrations and scaffoldings as slender structures are prone to such dynamic action. The method for determining the probability of vibrations excitation is presented here. The quantity representing this probability is called the predictor of occurrence of a dangerous situation due to vibrations induced by a walking employee. The predictor of resonance with ith natural frequency requires an analysis of the scaffolding dynamic behavior. The frequencies and the natural mode shapes of vibrations were determined. Numerical dynamic simulations of the worker's movement on the penultimate decks of two scaffoldings were carried out, as well. Predictor analysis was made for single frequencies and combinations of frequency pairs. The predictor values calculated for the first frequency or combinations with it are the highest ones, however the probability of resonance is not only affected by the first frequency. To improve safety, the natural frequencies should be increased. For longitudinal vibrations, this can be done by adding more bracing or reducing lengths of anchors. Increasing the number of anchors gives good results in both directions. During scaffolding design of both typical and atypical constructions, one must determine the natural frequencies and then, if the first natural frequency is less than 4.0 Hz, perform a dynamic scaffolding analysis.

Explanatory notes to the Geological map of Greenland, 1:500 000, Humboldt Gletscher, Sheet 6

2004 ◽  
pp. 1-48
Author(s):  
Peter R. Dawes
Keyword(s):  
Coarse Grained ◽  
Mobile Belt ◽  
Nares Strait ◽  
General Terms ◽  
Mineral Occurrence ◽  
North Eastern ◽  
Copper Gold ◽  
High Grade Metamorphism ◽  
Geological Map ◽  
Map Series

NOTE: This Map Description was published in a former series of GEUS Bulletin. Please use the original series name when citing this series, for example: Dawes, P. R. (2004). Explanatory notes to the Geological map of Greenland, 1:500 000, Humboldt Gletscher, Sheet 6. Geological Survey of Denmark and Greenland Map Series 1, 48 pp. + map. https://doi.org/10.34194/geusm.v1.4615  _______________ These explanatory notes cover the map region bounded by latitudes 78°N and 81°N and longitudes 56°W and 74°W, with geology shown on the land areas between Nares Strait - the seaway between Greenland and Ellesmere Island, Canada - and the Inland Ice. The bedrock geology is composed of Precambrian and Lower Palaeozoic provinces that continue across Nares Strait into Canada. Map units and mineral occurrences are described in general terms and are proceeded by sections on physical environment, logistics, data sources and geoscientific research. The notes are aimed at the practical user and a guide for further reading. The bedrock is composed of three provinces separated by unconformities, each representing a hiatus of c. 500 Ma during which basic dykes were emplaced. The Palaeoproterozoic Inglefield mobile belt, forming the crystalline shield, is an E-W-trending belt of deposition and orogeny characterised by polyphase magmatism, deformation and high-grade metamorphism. Clastic deposition, with magmatism at c. 1985 Ma, are the oldest events recorded, followed by the accumulation of the Etah Group (carbonate, pelitic and psammitic sediments with supposedly coeval mafic and ultramafic rocks) between 1980 and 1950 Ma ago. These rocks were intruded 1950 to 1915 Ma ago by the Etah meta-igneous complex, that records polyphase plutonism (intermediate to felsic, with some basic and magnetite-rich rocks), followed by deformation and partial melting producing granites 1785 to 1740 Ma ago. The Mesoproterozoic Thule Basin, defined by the unmetamorphosed and little deformed Thule Supergroup, records sedimentation and basaltic volcanism at least as old as 1270 Ma. The faulted, north-eastern basin margin shown on the map preserves the passage from the basinal sequence to a relatively thin platform succession invaded by basic sills. The Palaeozoic Franklinian Basin is represented by a homoclinal Cambrian to Silurian shelf carbonate succession and a major Silurian reef complex, with coeval siliciclastic slope deposits. The map region includes the classical area for Franklinian stratigraphy, now composed of 29 formations and four groups - Ryder Gletscher, Morris Bugt, Washington Land and Peary Land Groups. The only younger units preserved in the map region are widespread Quaternary deposits, an isolated outcrop of coarse-grained fluvial deposits (Bjørnehiet Formation) and non-carbonised wood erratics of Neogene age. Five mineral occurrence types are shown on the map: in lithologies of the Inglefield mobile belt, sulphide-graphite rust zones, a magnetite deposit and copper-gold mineralisation and in the Franklinian Basin, commercially drilled, zinc-lead-silver and zinc-lead-barium mineralisations. The basic ingredients of a petroleum model exist in the Franklinian Basin but prospectivity is low.

Quantifying the Predictive Skill in Long-Range Forecasting. Part II: Model Error in Coarse-Grained Markov Models with Application to Ocean-Circulation Regimes

2012 ◽  
Vol 25 (6) ◽  
pp. 1814-1826 ◽  
Author(s):  
Dimitrios Giannakis ◽  
Andrew J. Majda
Keyword(s):  
Long Range ◽  
Ocean Circulation ◽  
Climate Models ◽  
Markov Models ◽  
Low Frequency ◽  
Model Error ◽  
Ocean Model ◽  
Coarse Grained ◽  
Predictive Skill ◽  
Relaxation To Equilibrium

Abstract An information-theoretic framework is developed to assess the predictive skill and model error in imperfect climate models for long-range forecasting. Here, of key importance is a climate equilibrium consistency test for detecting false predictive skill, as well as an analogous criterion describing model error during relaxation to equilibrium. Climate equilibrium consistency enforces the requirement that long-range forecasting models should reproduce the climatology of prediction observables with high fidelity. If a model meets both climate consistency and the analogous criterion describing model error during relaxation to equilibrium, then relative entropy can be used as an unbiased superensemble measure of the model’s skill in long-range coarse-grained forecasts. As an application, the authors investigate the error in modeling regime transitions in a 1.5-layer ocean model as a Markov process and identify models that are strongly persistent but their predictive skill is false. The general techniques developed here are also useful for estimating predictive skill with model error for Markov models of low-frequency atmospheric regimes.

Monitoring Changes in the Soil and Foundation Characteristics of an Offshore Wind Turbine Using Automated Operational Modal Analysis

2013 ◽  
Vol 569-570 ◽  
pp. 652-659 ◽  
Author(s):  
Gert de Sitter ◽  
Wout Weitjens ◽  
Mahmoud El-Kafafy ◽  
Christof Devriendt
Keyword(s):  
Wind Turbine ◽  
Modal Analysis ◽  
Continuous Monitoring ◽  
Low Frequency ◽  
Operational Modal Analysis ◽  
Human Interaction ◽  
Offshore Wind ◽  
Offshore Wind Turbine ◽  
Support Structure ◽  
Lower Natural Frequency

This paper will show the first results of a long term monitoring campaign on an offshore wind turbine in the Belgian North Sea. It will focus on the vibration levels and resonant frequencies of the fundamental modes of the support structure. These parameters will be crucial to minimize O&M costs and to extend the lifetime of offshore wind turbine structures. For monopile foundations for example, scouring and reduction in foundation integrity over time are especially problematic because they reduce the fundamental structural resonance of the support structure, aligning that resonance frequency more closely to the lower frequencies. Since both the broadband wave energy and the rotating frequency of the turbine are contained in this low frequency band, the lower natural frequency can create resonant behavior increasing fatigue damage. Continuous monitoring of the effect of scour on the dynamics of the wind turbine will help to optimize the maintenance activities on the scour protection system. To allow a proper continuous monitoring during operation, reliable state-of-the-art operational modal analysis techniques should be used and these are presented in this paper. The methods are also automated, so that no human-interaction is required and the system can track the natural frequencies and damping ratios in a reliable manner.

scholarly journals Dynamics and Protein–Solvent Interactions of Hemoglobin in T and R Quaternary Conformation

2002 ◽  
Vol 16 (3-4) ◽  
pp. 227-233 ◽  
Author(s):  
Chiara Caronna ◽  
Antonio Cupane
Keyword(s):  
Quaternary Structure ◽  
Dynamic Properties ◽  
Low Frequency ◽  
Helical Structure ◽  
Blue Shift ◽  
Peak Frequency ◽  
The Other ◽  
Solvent Interactions ◽  
Reported Data ◽  
Increasing Temperature

In this work we report the thermal behaviour of the amide I′ band of carbonmonoxy and deoxy hemoglobin in 65% v/v glycerolD8/D2O solutions and in the temperature interval 10–295 K. Following recent suggestions in the literature, we analyze the amide I′ band in terms of two components, one at about 1630 cm−1and the other at about 1650 cm−1, that are assigned to solvent‒exposed and buried α‒helical regions, respectively.For deoxy hemoglobin (in T quaternary structure) both components are narrower with respect to carbonmonoxy hemoglobin (in R quaternary structure), while the peak frequency blue shift observed, upon increasing temperature, for the component at about 1630 cm−1is smaller. The reported data provide evidence of the dependence of hemoglobin dynamic properties upon the protein quaternary structure and suggest a more compact α‒helical structure of hemoglobin in T conformation, with reduced population of low‒frequency modes involving the solvent and protein.

A new spectral coarse-graining algorithm based on K-means clustering in complex networks

2019 ◽  
Vol 33 (01) ◽  
pp. 1850421 ◽  
Author(s):  
Lang Zeng ◽  
Zhen Jia ◽  
Yingying Wang
Keyword(s):  
Complex Networks ◽  
Large Scale ◽  
Dynamic Properties ◽  
Coarse Graining ◽  
Kuramoto Model ◽  
Coarse Grained ◽  
Original Network ◽  
Topological Information ◽  
Real World Applications ◽  
Large Scale Networks

Coarse-graining of complex networks is one of the important algorithms to study large-scale networks, which is committed to reducing the size of networks while preserving some topological information or dynamic properties of the original networks. Spectral coarse-graining (SCG) is one of the typical coarse-graining algorithms, which can keep the synchronization ability of the original network well. However, the calculation of SCG is large, which limits its real-world applications. And it is difficult to accurately control the scale of the coarse-grained network. In this paper, a new SCG algorithm based on K-means clustering (KCSCG) is proposed, which cannot only reduce the amount of calculation, but also accurately control the size of coarse-grained network. At the same time, KCSCG algorithm has better effect in keeping the network synchronization ability than SCG algorithm. A large number of numerical simulations and Kuramoto-model example on several typical networks verify the feasibility and effectiveness of the proposed algorithm.

scholarly journals Combined approach architecture development to simulation modeling of systems with parallelism

2021 ◽  
Vol 4 (4(112)) ◽  
pp. 74-82
Author(s):  
Oksana Suprunenko
Keyword(s):  
Petri Nets ◽  
Dynamic Properties ◽  
Discrete Event ◽  
Structural Similarity ◽  
Integral Model ◽  
Combined Approach ◽  
Dynamic Simulations ◽  
Holistic Model ◽  
Event Modeling ◽  
Analytical Tools

Paradigms and graphical-analytical tools for building simulation tools and forming the architecture of a combined approach to studying the dynamic properties of systems with parallelism are described. An extension of the formal language of Petri nets is presented, which has greater modeling power than WF nets. The properties of hierarchical Petri nets are used to synthesize a holistic model. Discrete-event modeling and modeling of dynamic systems, which allow reflecting the quantitative and qualitative characteristics of the elements of the systems under study, served as the basis for the combined approach to the simulation of systems with parallelism. On their basis, graphic-analytical tools are proposed that provide the ability to describe the modeled system, adhering to the principle of structural similarity. They have dynamic simulations that make it easy to visually analyze and correct the model. Also, the proposed toolkit provides for the analysis of the dynamic properties of the model, which makes it possible to identify accumulated phenomena that can lead to unpredictability of the system’s functioning. A conceptual model for the synthesis and analysis of systems with parallelism is proposed, which provides for the construction of the components of the model based on the architecture. Their step-by-step analysis and the formation of an integral model of the software system are carried out using a network representation, according to the matrix description of which invariants are calculated. The analysis of invariants allows one to obtain the dynamic properties of the model and determine the localization of structures that lead to critical situations when they are detected. The architecture of the combined approach to the simulation of systems with parallelism is built, which provides the study of their dynamic properties to improve the reliability of the functioning of software systems

scholarly journals An individual-based mechanical model of cell movement in heterogeneous tissues and its coarse-grained approximation

2018 ◽  
Author(s):  
R. J. Murphy ◽  
P. R. Buenzli ◽  
R. E. Baker ◽  
M. J. Simpson
Keyword(s):  
Mechanical Model ◽  
Numerical Solutions ◽  
Cell Movement ◽  
Biological Tissues ◽  
Tissue Level ◽  
Cellular Level ◽  
Coarse Grained ◽  
Mechanical Heterogeneity ◽  
Single Scale ◽  
The Individual

AbstractMechanical heterogeneity in biological tissues, in particular stiffness, can be used to distinguish between healthy and diseased states. However, it is often difficult to explore relationships between cellular-level properties and tissue-level outcomes when biological experiments are performed at a single scale only. To overcome this difficulty we develop a multi-scale mathematical model which provides a clear framework to explore these connections across biological scales. Starting with an individual-based mechanical model of cell movement, we subsequently derive a novel coarse-grained system of partial differential equations governing the evolution of the cell density due to heterogeneous cellular properties. We demonstrate that solutions of the individual-based model converge to numerical solutions of the coarse-grained model, for both slowly-varying-in-space and rapidly-varying-in-space cellular properties. Applications of the model are discussed, including determining relative cellular-level properties and an interpretation of data from a breast cancer detection experiment.

Sign in / Sign up

Export Citation Format

Share Document