scholarly journals Understanding contagion dynamics through microscopic processes in active Brownian particles

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Ariel Norambuena ◽  
Felipe J. Valencia ◽  
Francisca Guzmán-Lastra
Keyword(s):  
First Principles ◽  
Horizontal Transmission ◽  
Sir Model ◽  
Virus Spread ◽  
Interacting Particles ◽  
Brownian Particles ◽  
Wide Range ◽  
Recovery Times ◽  
Average Description ◽  
Free Parameters

AbstractTogether with the universally recognized SIR model, several approaches have been employed to understand the contagion dynamics of interacting particles. Here, Active Brownian particles (ABP) are introduced to model the contagion dynamics of living agents that perform a horizontal transmission of an infectious disease in space and time. By performing an ensemble average description of the ABP simulations, we statistically describe susceptible, infected, and recovered groups in terms of particle densities, activity, contagious rates, and random recovery times. Our results show that ABP reproduces the time dependence observed in traditional compartmental models such as the Susceptible-Infected-Recovery (SIR) models and allows us to explore the critical densities and the contagious radius that facilitates the virus spread. Furthermore, we derive a first-principles analytical expression for the contagion rate in terms of microscopic parameters, without considering free parameters as the classical SIR-based models. This approach offers a novel alternative to incorporate microscopic processes into analyzing SIR-based models with applications in a wide range of biological systems.

Combining First-Principles and Data Modeling for the Accurate Prediction of the Refractive Index of Organic Polymers

2017 ◽  
Author(s):  
Mohammad Atif Faiz Afzal ◽  
Chong Cheng ◽  
Johannes Hachmann
Keyword(s):  
First Principles ◽  
Data Modeling ◽  
Accurate Prediction ◽  
Index Of Refraction ◽  
Structure Theory ◽  
Organic Polymers ◽  
Number Density ◽  
Lorenz Equation ◽  
In Silico Studies ◽  
Wide Range

Organic materials with a high index of refraction (RI) are attracting considerable interest due to their potential application in optic and optoelectronic devices. However, most of these applications require an RI value of 1.7 or larger, while typical carbon-based polymers only exhibit values in the range of 1.3–1.5. This paper introduces an efficient computational protocol for the accurate prediction of RI values in polymers to facilitate in silico studies that an guide the discovery and design of next-generation high-RI materials. Our protocol is based on the Lorentz-Lorenz equation and is parametrized by the polarizability and number density values of a given candidate compound. In the proposed scheme, we compute the former using first-principles electronic structure theory and the latter using an approximation based on van der Waals volumes. The critical parameter in the number density approximation is the packing fraction of the bulk polymer, for which we have devised a machine learning model. We demonstrate the performance of the proposed RI protocol by testing its predictions against the experimentally known RI values of 112 optical polymers. Our approach to combine first-principles and data modeling emerges as both a successful and highly economical path to determining the RI values for a wide range of organic polymers.

scholarly journals Clustering Single-Cell RNA-Seq Data with Regularized Gaussian Graphical Model

Genes ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 311
Author(s):  
Zhenqiu Liu
Keyword(s):  
Single Cell ◽  
Free Parameter ◽  
Graphical Model ◽  
Expression Patterns ◽  
Information Criterion ◽  
Log P ◽  
Rna Seq ◽  
Clustering Methods ◽  
Wide Range ◽  
Free Parameters

Single-cell RNA-seq (scRNA-seq) is a powerful tool to measure the expression patterns of individual cells and discover heterogeneity and functional diversity among cell populations. Due to variability, it is challenging to analyze such data efficiently. Many clustering methods have been developed using at least one free parameter. Different choices for free parameters may lead to substantially different visualizations and clusters. Tuning free parameters is also time consuming. Thus there is need for a simple, robust, and efficient clustering method. In this paper, we propose a new regularized Gaussian graphical clustering (RGGC) method for scRNA-seq data. RGGC is based on high-order (partial) correlations and subspace learning, and is robust over a wide-range of a regularized parameter λ. Therefore, we can simply set λ=2 or λ=log(p) for AIC (Akaike information criterion) or BIC (Bayesian information criterion) without cross-validation. Cell subpopulations are discovered by the Louvain community detection algorithm that determines the number of clusters automatically. There is no free parameter to be tuned with RGGC. When evaluated with simulated and benchmark scRNA-seq data sets against widely used methods, RGGC is computationally efficient and one of the top performers. It can detect inter-sample cell heterogeneity, when applied to glioblastoma scRNA-seq data.

Stability and Structures of Constitutional Defects in Nonstoichiometric Intermetallic Compounds by First-Principles Calculations

2005 ◽  
Vol 475-479 ◽  
pp. 3111-3114
Author(s):  
Masataka Mizuno ◽  
Hideki Araki ◽  
Yasuharu Shirai
Keyword(s):  
Intermetallic Compounds ◽  
First Principles ◽  
Electronic Structures ◽  
Stoichiometric Composition ◽  
Electronic Structure Calculations ◽  
First Principles Calculations ◽  
Compositional Dependence ◽  
Wide Range ◽  
Formation Energies ◽  
Structure Calculations

Some of intermetallic compounds exist in a wide range of concentration around the stoichiometric composition. First-principles electronic structure calculations have been performed for constitutional defects in non-stoichiometric CoAl and CoTi in order to investigate their stabilities and structural relaxations induced by constitutional defects. For the evaluation of stabilities of constitutional defects, the compositional dependence curves both of formation energies and of lattice parameters are obtained by the calculations employing supercells in various sizes. The lattice relaxations around constitutional defects are discussed by analyzing the change in electronic structures induced by constitutional defects.

First-Principles Studies of the Magnetic Properties of hcp Cr in Cr/Cu(111) and Cr/Ru(0001) Superlattices

2002 ◽  
Vol 721 ◽  
Author(s):  
G. Y. Guo
Keyword(s):  
First Principles ◽  
Density Functional ◽  
Recent Observation ◽  
Theoretical Calculations ◽  
Ferromagnetic State ◽  
Full Potential ◽  
Generalized Gradient ◽  
Plane Wave Method ◽  
Wide Range ◽  
Linearized Augmented Plane Wave

AbstractLatest first-principles density functional theoretical calculations using the generalized gradient approximation and highly accurate all-eleectron full-potential linearized augmented plane wave method, show that bulk hcp Cr would be a paramagnet and that no ferromagnetic state could be stabilized over a wide range of volume [1]. To understand the recent observation of the weakly ferromagnetic state of Cr in hcp Cr/Ru (0001) superlattices [2], the same theoretical calculations have been carried out for the hcp Cr3/Ru7 (0001) and hcp Cr3/fcc Cu6 (111) superlattices. The Cr/Ru superlattice is found to be ferromagnetic with a small magnetic moment of ∼0.31μB/Cr while in contrast, Cr/Cu superlattice is found to be nonmagnetic.

scholarly journals Eighth Order Two-Step Methods Trained to Perform Better on Keplerian-Type Orbits

Mathematics ◽  
2021 ◽  
Vol 9 (23) ◽  
pp. 3071
Author(s):  
Vladislav N. Kovalnogov ◽  
Ruslan V. Fedorov ◽  
Andrey V. Chukalin ◽  
Theodore E. Simos ◽  
Charalampos Tsitouras
Keyword(s):  
Differential Evolution ◽  
Eighth Order ◽  
Numerical Tests ◽  
Wide Range ◽  
The Family ◽  
Free Parameters

The family of Numerov-type methods that effectively uses seven stages per step is considered. All the coefficients of the methods belonging to this family can be expressed analytically with respect to four free parameters. These coefficients are trained through a differential evolution technique in order to perform best in a wide range of Keplerian-type orbits. Then it is observed with extended numerical tests that a certain method behaves extremely well in a variety of orbits (e.g., Kepler, perturbed Kepler, Arenstorf, Pleiades) for various steplengths used by the methods and for various intervals of integration.

scholarly journals Tuning the electronic properties of monolayer and bilayer PtSe2via strain engineering

2016 ◽  
Vol 4 (15) ◽  
pp. 3106-3112 ◽  
Author(s):  
Pengfei Li ◽  
Lei Li ◽  
Xiao Cheng Zeng
Keyword(s):  
Electronic Properties ◽  
First Principles ◽  
Strain Engineering ◽  
Band Gaps ◽  
Wide Range

Based on the first-principles computations we show that the band gaps of monolayer and bilayer PtSe2 can be tuned over a wide range via strain engineering.

scholarly journals A class of three-dimensional gyroviscous magnetohydrodynamic models

2020 ◽  
Vol 86 (5) ◽  
Author(s):  
Manasvi Lingam ◽  
Philip J. Morrison ◽  
Alexander Wurm
Keyword(s):  
First Principles ◽  
Three Dimensional ◽  
Action Principle ◽  
Wide Range ◽  
Magnetohydrodynamic Models

A Hamiltonian and action principle formalism for deriving three-dimensional gyroviscous magnetohydrodynamic models is presented. The uniqueness of the approach in constructing the gyroviscous tensor from first principles and its ability to explain the origin of the gyromap and the gyroviscous terms are highlighted. The procedure allows for the specification of free functions, which can be used to generate a wide range of gyroviscous models. Through the process of reduction, the noncanonical Hamiltonian bracket is obtained and briefly analysed.

scholarly journals A First-Principles Study of Nonlinear Elastic Behavior and Anisotropic Electronic Properties of Two-Dimensional HfS2

Nanomaterials ◽  
2020 ◽  
Vol 10 (3) ◽  
pp. 446
Author(s):  
Mahdi Faghihnasiri ◽  
Aidin Ahmadi ◽  
Samaneh Alvankar Golpayegan ◽  
Saeideh Garosi Sharifabadi ◽  
Ali Ramazani
Keyword(s):  
Electronic Properties ◽  
First Principles ◽  
Electronic Band Structure ◽  
Hexagonal Phase ◽  
Strain Engineering ◽  
Elastic Behavior ◽  
Potential Candidate ◽  
Two Dimensional ◽  
Electronic Band ◽  
Wide Range

We utilize first principles calculations to investigate the mechanical properties and strain-dependent electronic band structure of the hexagonal phase of two dimensional (2D) HfS2. We apply three different deformation modes within −10% to 30% range of two uniaxial (D1, D2) and one biaxial (D3) strains along x, y, and x-y directions, respectively. The harmonic regions are identified in each deformation mode. The ultimate stress for D1, D2, and D3 deformations is obtained as 0.037, 0.038 and 0.044 (eV/Ang3), respectively. Additionally, the ultimate strain for D1, D2, and D3 deformation is obtained as 17.2, 17.51, and 21.17 (eV/Ang3), respectively. In the next step, we determine the second-, third-, and fourth-order elastic constants and the electronic properties of both unstrained and strained HfS2 monolayers are investigated. Our findings reveal that the unstrained HfS2 monolayer is a semiconductor with an indirect bandgap of 1.12 eV. We then tune the bandgap of HfS2 with strain engineering. Our findings reveal how to tune and control the electronic properties of HfS2 monolayer with strain engineering, and make it a potential candidate for a wide range of applications including photovoltaics, electronics and optoelectronics.

scholarly journals Evolution of early male-killing in horizontally transmitted parasites

2015 ◽  
Vol 282 (1818) ◽  
pp. 20152068 ◽  
Author(s):  
Veronika Bernhauerová ◽  
Luděk Berec ◽  
Daniel Maxin
Keyword(s):  
Empirical Evidence ◽  
Vertical Transmission ◽  
Bacterial Strain ◽  
Horizontal Transmission ◽  
Distinct Species ◽  
High Efficacy ◽  
Infected Male ◽  
Male Killing ◽  
Wide Range ◽  
Male Killer

Early male-killing (MK) bacteria are vertically transmitted reproductive parasites which kill male offspring that inherit them. Whereas their incidence is well documented, characteristics allowing originally non-MK bacteria to gradually evolve MK ability remain unclear. We show that horizontal transmission is a mechanism enabling vertically transmitted bacteria to evolve fully efficient MK under a wide range of host and parasite characteristics, especially when the efficacy of vertical transmission is high. We also show that an almost 100% vertically transmitted and 100% effective male-killer may evolve from a purely horizontally transmitted non-MK ancestor, and that a 100% efficient male-killer can form a stable coexistence only with a non-MK bacterial strain. Our findings are in line with the empirical evidence on current MK bacteria, explain their high efficacy in killing infected male embryos and their variability within and across insect taxa, and suggest that they may have evolved independently in phylogenetically distinct species.

A Natural Convection Fin with a Solution-Determined Nonmonotonically Varying Heat Transfer Coefficient

1981 ◽  
Vol 103 (2) ◽  
pp. 218-225 ◽  
Author(s):  
E. M. Sparrow ◽  
S. Acharya
Keyword(s):  
Heat Transfer ◽  
Heat Transfer Coefficient ◽  
Natural Convection ◽  
Transfer Coefficient ◽  
First Principles ◽  
Numerical Solutions ◽  
Flow Direction ◽  
Operating Conditions ◽  
Fluid Temperature ◽  
Wide Range

A conjugate conduction-convection analysis has been made for a vertical plate fin which exchanges heat with its fluid environment by natural convection. The analysis is based on a first-principles approach whereby the heat conduction equation for the fin is solved simultaneously with the conservation equations for mass, momentum, and energy in the fluid boundary layer adjacent to the fin. The natural convection heat transfer coefficient is not specified in advance but is one of the results of the numerical solutions. For a wide range of operating conditions, the local heat transfer coefficients were found not to decrease monotonically in the flow direction, as is usual. Rather, the coefficient decreased at first, attained a minimum, and then increased with increasing downstream distance. This behavior was attributed to an enhanced buoyancy resulting from an increase in the wall-to-fluid temperature difference along the streamwise direction. To supplement the first-principles analysis, results were also obtained from a simple adaptation of the conventional fin model.

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