scholarly journals Protobiotic Systems Chemistry Analyzed by Molecular Dynamics

Life ◽  
2019 ◽  
Vol 9 (2) ◽  
pp. 38 ◽  
Author(s):  
Amit Kahana ◽  
Doron Lancet
Keyword(s):  
Molecular Dynamics ◽  
Molecular Networks ◽  
Biological Phenomena ◽  
Systems Chemistry ◽  
Lipid World ◽  
Replication Domain ◽  
Definition Of ◽  
Micellar Formation ◽  
Dynamics Analyses ◽  
Changes Over Time

Systems chemistry has been a key component of origin of life research, invoking models of life’s inception based on evolving molecular networks. One such model is the graded autocatalysis replication domain (GARD) formalism embodied in a lipid world scenario, which offers rigorous computer simulation based on defined chemical kinetics equations. GARD suggests that the first pre-RNA life-like entities could have been homeostatically-growing assemblies of amphiphiles, undergoing compositional replication and mutations, as well as rudimentary selection and evolution. Recent progress in molecular dynamics has provided an experimental tool to study complex biological phenomena such as protein folding, ligand-receptor interactions, and micellar formation, growth, and fission. The detailed molecular definition of GARD and its inter-molecular catalytic interactions make it highly compatible with molecular dynamics analyses. We present a roadmap for simulating GARD’s kinetic and thermodynamic behavior using various molecular dynamics methodologies. We review different approaches for testing the validity of the GARD model by following micellar accretion and fission events and examining compositional changes over time. Near-future computational advances could provide empirical delineation for further system complexification, from simple compositional non-covalent assemblies towards more life-like protocellular entities with covalent chemistry that underlies metabolism and genetic encoding.

scholarly journals Protobiotic Systems Chemistry Analyzed by Molecular Dynamics

2019 ◽  
Author(s):  
Amit Kahana ◽  
Doron Lancet
Keyword(s):  
Molecular Dynamics ◽  
Molecular Networks ◽  
Biological Phenomena ◽  
Systems Chemistry ◽  
Lipid World ◽  
Replication Domain ◽  
Definition Of ◽  
Micellar Formation ◽  
Dynamics Analyses ◽  
Changes Over Time

Systems Chemistry has been a key component of origin of life research, invoking models of life’s inception based on evolving molecular networks. One such model is the Graded Autocatalysis Replication Domain (GARD) formalism embodied in a Lipid World scenario, which offers rigorous computer simulation based on defined chemical kinetics equations. GARD suggests that the first pre-RNA life-like entities could have been homeostatically-growing assemblies of amphiphiles, undergoing compositional replication and mutations, as well as rudimentary selection and evolution. Recent progress in Molecular Dynamics has provided an experimental tool to study complex biological phenomena such as protein folding, ligand-receptor interactions and micellar formation, growth and fission. The detailed molecular definition of GARD and its inter-molecular catalytic interactions make it highly compatible with Molecular Dynamics analyses. We present a roadmap for simulating GARD’s kinetic and thermodynamic behavior using various Molecular Dynamics methodologies. We review different approaches for testing the validity of the GARD model, by following micellar accretion and fission events and examining compositional changes over time. Near future computational advances could provide empirical delineation for further system complexification, from simple compositional non-covalent assemblies towards more life-like protocellular entities with covalent chemistry that underlies metabolism and genetic encoding.

Fundamental relations and identities of fuzzy hyperalgebras

2021 ◽  
pp. 1-10
Author(s):  
Narjes Firouzkouhi ◽  
Abbas Amini ◽  
Chun Cheng ◽  
Mehdi Soleymani ◽  
Bijan Davvaz
Keyword(s):  
Universal Algebra ◽  
Equivalence Relation ◽  
Polynomial Function ◽  
Equivalence Relations ◽  
Fundamental Relation ◽  
Term Function ◽  
Biological Phenomena ◽  
Definition Of

Inspired by fuzzy hyperalgebras and fuzzy polynomial function (term function), some homomorphism properties of fundamental relation on fuzzy hyperalgebras are conveyed. The obtained relations of fuzzy hyperalgebra are utilized for certain applications, i.e., biological phenomena and genetics along with some elucidatory examples presenting various aspects of fuzzy hyperalgebras. Then, by considering the definition of identities (weak and strong) as a class of fuzzy polynomial function, the smallest equivalence relation (fundamental relation) is obtained which is an important tool for fuzzy hyperalgebraic systems. Through the characterization of these equivalence relations of a fuzzy hyperalgebra, we assign the smallest equivalence relation α i 1 i 2 ∗ on a fuzzy hyperalgebra via identities where the factor hyperalgebra is a universal algebra. We extend and improve the identities on fuzzy hyperalgebras and characterize the smallest equivalence relation α J ∗ on the set of strong identities.

scholarly journals The Polish Experience in the Development of Smart Cities

2021 ◽  
Vol 11 (2) ◽  
pp. 48-64
Author(s):  
Magdalena Kisała
Keyword(s):  
Smart City ◽  
Smart Cities ◽  
Urban Spaces ◽  
Polish Experience ◽  
The Subject ◽  
Universal Definition ◽  
Definition Of ◽  
Urban Population Growth ◽  
Changes Over Time ◽  
Beneficial Approach

Abstract In recent years, Poland has seen an increased migration of people to cities, which translates into significant urban population growth. This, in turn, raises new challenges in the performance of cities’ tasks and responsibilities. Additionally, climate changes and the depletion of natural resources necessitate the modification of existing urban practices. Polish cities seek solutions which would enable social, economic and environmental demands to be reconciled so that urban spaces become friendly for the city’s inhabitants and investors. Some Polish cities have applied the smart city concept to solve their problems. Despite the fact that the concept has been the subject of scientific research for many years, no universal definition of the smart city has been agreed upon. Analyzed assumptions of the smart city concept as well as the Polish experiences in the implementation indicate that the concept is dynamic and changes over time. It should be considered as a perpetual process unrestricted by a specific timeframe. This impedes the formulation of uniform, generally accepted assumptions of the concept since its existence is inscribed in the change related to urban development. This article claims that this would be a beneficial approach for formulating the general characteristics of the smart city that could be applicable to any city, and that could be employed regardless of the present challenges cities may face.

Construction of an Indicator System for Integrated Assessment of Environmental Quality of the Dianchi Basin

2011 ◽  
Vol 356-360 ◽  
pp. 903-907
Author(s):  
Ai Jun Li ◽  
Yan Ying Guo ◽  
Feng He ◽  
Rui Jia Yuan
Keyword(s):  
Environmental Quality ◽  
Integrated Assessment ◽  
Large Scale ◽  
Environmental Changes ◽  
Indicator System ◽  
Regional Environment ◽  
Definition Of ◽  
Changes Over Time ◽  
Regional Environmental Quality

There are few indicator systems available for monitoring and assessing the environmental quality of large-scale regions. We constructed an indicator system for integrated assessment of the environmental quality of the Dianchi Basin. First, the definition of regional environmental quality is determined by both the supply of materials and energy in the region and the extent to which the region is polluted. Second, the indicator categories used for assessment mainly comprise vegetation biomass and the concentrations of various pollutants. Third, owing to spatial heterogeneity of a region, evaluation of the regional environment first requires division into sub-regions, each of which should be relatively homogeneous with regard to physical conditions (e.g. marine and terrestrial) and appearance (e.g. vegetation cover). Finally, the mathematical models for assessing regional environmental quality can be built according to the relationships between the various indicators, the sub-regions and regional environmental quality. The indicator system built using this approach can reflect environmental changes over time and identifies reasons for environmental variation.

scholarly journals Validity of the molecular-dynamics-lattice-gas global equilibrium distribution function

2019 ◽  
Vol 30 (10) ◽  
pp. 1941007 ◽  
Author(s):  
M. Reza Parsa ◽  
Aleksandra Pachalieva ◽  
Alexander J. Wagner
Keyword(s):  
Molecular Dynamics ◽  
Distribution Function ◽  
Lattice Gas ◽  
Equilibrium Distribution ◽  
Coarse Graining ◽  
High Volume ◽  
Equilibrium Distribution Function ◽  
Theory Approach ◽  
Lattice Boltzmann Methods ◽  
Definition Of

The molecular-dynamics-lattice-gas (MDLG) method establishes a direct link between a lattice-gas method and the coarse-graining of a molecular dynamics (MD) approach. Due to its connection to MD, the MDLG rigorously recovers the hydrodynamics and allows to validate the behavior of the lattice-gas or lattice-Boltzmann methods directly without using the standard kinetic theory approach. In this paper, we show that the analytical definition of the equilibrium distribution function remains valid even for very high volume fractions.

scholarly journals Investigating the Effect of Solid Boundaries on the Gas Molecular Mean-Free-Path

2009 ◽  
Author(s):  
Erik J. Arlemark ◽  
Jason M. Reese
Keyword(s):  
Molecular Dynamics ◽  
Boundary Conditions ◽  
Free Path ◽  
Mean Free Path ◽  
Gas Flows ◽  
Standard Temperature ◽  
Binary Collisions ◽  
The Mean ◽  
Temperature And Pressure ◽  
Definition Of

A key parameter for micro-gas-flows, the mean free path, is investigated in this paper. The mean free path is used in various models for predicting micro gas flows, both in the governing equations and their boundary conditions. The conventional definition of the mean free path is based on the assumption that only binary collisions occur and is commonly described using the macroscopic quantities density, viscosity and temperature. In this paper we compare the prediction by this definition of the mean free paths for helium, neon and argon gases under standard temperature and pressure conditions, with the mean free paths achieved by measurements of individual molecules using the numerical simulation technique of molecular dynamics. Our simulation using molecular dynamics consists of a cube with six periodic boundary conditions, allowing us to simulate an unconfined gas “package”. Although, the size of this package is important, since its impact on computational cost is considerable, it is also important to have enough simulated molecules to average data from. We find that the molecular dynamics method using 20520 simulated molecules yields results that are within 1% accuracy from the conventional definition of the mean free paths for neon and argon and within 2.5% for helium. We can also conclude that the normal approximation of only considering binary collisions is seemingly adequate for these gases under standard temperature and pressure conditions. We introduce a single planar wall and two parallel planar walls to the simulated gas of neon and record the mean free paths at various distances to the walls. It is found that the mean free paths affected by molecular collisions with the walls corresponds well with theoretical models up to Knudsen numbers of 0.2.

scholarly journals Surface energy of nanoparticles – influence of particle size and structure

2018 ◽  
Vol 9 ◽  
pp. 2265-2276 ◽  
Author(s):  
Dieter Vollath ◽  
Franz Dieter Fischer ◽  
David Holec
Keyword(s):  
Molecular Dynamics ◽  
Particle Size ◽  
Surface Energy ◽  
Ab Initio Calculations ◽  
Ab Initio ◽  
Molecular Dynamics Simulations ◽  
Definition Of ◽  
Dynamics Simulations ◽  
Classical Thermodynamics ◽  
A Minor

The surface energy, particularly for nanoparticles, is one of the most important quantities in understanding the thermodynamics of particles. Therefore, it is astonishing that there is still great uncertainty about its value. The uncertainty increases if one questions its dependence on particle size. Different approaches, such as classical thermodynamics calculations, molecular dynamics simulations, and ab initio calculations, exist to predict this quantity. Generally, considerations based on classical thermodynamics lead to the prediction of decreasing values of the surface energy with decreasing particle size. This phenomenon is caused by the reduced number of next neighbors of surface atoms with decreasing particle size, a phenomenon that is partly compensated by the reduction of the binding energy between the atoms with decreasing particle size. Furthermore, this compensating effect may be expected by the formation of a disordered or quasi-liquid layer at the surface. The atomistic approach, based either on molecular dynamics simulations or ab initio calculations, generally leads to values with an opposite tendency. However, it is shown that this result is based on an insufficient definition of the particle size. A more realistic definition of the particle size is possible only by a detailed analysis of the electronic structure obtained from initio calculations. Except for minor variations caused by changes in the structure, only a minor dependence of the surface energy on the particle size is found. The main conclusion of this work is that surface energy values for the equivalent bulk materials should be used if detailed data for nanoparticles are not available.

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