Entropy and Entropic Forces to Model Biological Fluids

Living cells are complex systems characterized by fluids crowded by hundreds of different elements, including, in particular, a high density of polymers. They are an excellent and challenging laboratory to study exotic emerging physical phenomena, where entropic forces emerge from the organization processes of many-body interactions. The competition between microscopic and entropic forces may generate complex behaviors, such as phase transitions, which living cells may use to accomplish their functions. In the era of big data, where biological information abounds, but general principles and precise understanding of the microscopic interactions is scarce, entropy methods may offer significant information. In this work, we developed a model where a complex thermodynamic equilibrium resulted from the competition between an effective electrostatic short-range interaction and the entropic forces emerging in a fluid crowded by different sized polymers. The target audience for this article are interdisciplinary researchers in complex systems, particularly in thermodynamics and biophysics modeling.

Download Full-text

Entropy and Entropic Forces to Model Biological Fluids

10.20944/preprints202107.0309.v1 ◽

2021 ◽

Author(s):

Rafael M. Gutierrez ◽

George T. Shubeita ◽

Chandrashekhar U. Murade ◽

Jianfeng Guo

Keyword(s):

Complex Systems ◽

Biological Fluids ◽

Living Cells ◽

Biological Information ◽

Many Body ◽

Significant Information ◽

Precise Understanding ◽

Microscopic Interactions ◽

Physical Phenomena ◽

Many Body Interactions

Living cells are complex systems that may be characterized by fluids crowded by hundreds of different elements in particular by a high density of polymers; they are an excellent and challenging laboratory to study exotic emerging physical phenomena where entropic forces emerge from organization processes of many-body interactions. The competition between microscopic and entropic forces may generate complex behaviors like phase transitions that living cells may use to accomplish their functions. In the era of the big data, when biological information abounds but general principles and precise understanding of the microscopic interactions scarce, the entropy methods may offer significant information. In this work we develop a model where the thermodynamic equilibrium results from the competition between an effective electrostatic shortrange interaction and the entropic forces emerging in a fluid crowded by different size polymers. The target audience for this article are interdisciplinary researchers in complex systems, particularly in thermodynamics and biophysics modeling.

Download Full-text

Coexisting Ordering and Phase Separation in Binary Fcc Alloys

MRS Proceedings ◽

10.1557/proc-21-481 ◽

1982 ◽

Vol 21 ◽

Cited By ~ 2

Author(s):

P.L. Rossiter ◽

P.J. Lawrence

Keyword(s):

Miscibility Gap ◽

Nearest Neighbour ◽

Many Body ◽

Range Interaction ◽

Slow Cooling ◽

Pairwise Interactions ◽

Fcc Alloys ◽

Many Body Interactions ◽

Comparable Magnitude

ABSTRACTConsideration of only nearest neighbour pairwise interactions Vij in a binary alloy leads to the classification of the system as ordering (unlike near neighbours) or clustering (like near neighbours), depending upon the sign of Vij However, this simple classification loses meaning when multi-atom correlations, many-body interactions or a longer range interaction are considered. For example, the first nearest neighbour interaction may favour ordering while the second, which may be of comparable magnitude, may favour clustering. By extending the Bragg-Williams model to include second near-neighbour interactions in fcc alloys, it is shown that a miscibility gap may form in the region of the orderdisorder solvus, leading to a complicated sequence of atomicrearrangement upon slow cooling. Despite the well-known failings of the point approximation when applied to fcc alloys, the results are shown to be consistent with the unusual behaviour exhibited by some systems.

Download Full-text

Equation of state of asymmetric nuclear matter: a VMC study

Open Physics ◽

10.2478/s11534-009-0129-2 ◽

2010 ◽

Vol 8 (4) ◽

Cited By ~ 4

Author(s):

Kaan Manisa ◽

Ülfet Atav ◽

Sibel Sarıaydın

Keyword(s):

Nuclear Matter ◽

Many Body ◽

Isospin Asymmetry ◽

Asymmetric Nuclear Matter ◽

Methods And Techniques ◽

Microscopic Interactions ◽

Many Body Interactions ◽

Asymmetry Parameters ◽

Kinetic And Potential Energies ◽

Good Agreement

AbstractA Variational Monte Carlo (VMC) method is employed to investigate the properties of symmetric and asymmetric nuclear matter. The realistic Urbana V 14 twonucleon interaction potential of Lagaris and Pandharipande was used to describe the microscopic interactions. Also, many body interactions are included as a density dependent term in the potential. Total kinetic and potential energies per particle are calculated for asymmetric nuclear matter by VMC method at various densities and isospin asymmetry parameters. The results are compared with data found in literature, and it was observed that the results obtained in this study reasonably agree with the results found in the literature. Also, the symmetry energy and incompressibility factor of the nuclear matter were obtained. The results obtained are in good agreement with those obtained by various authors with different methods and techniques.

Download Full-text

Bond order redefinition needed to reduce inherent noise in molecular dynamics simulations

Scientific Reports ◽

10.1038/s41598-020-80217-0 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Ibnu Syuhada ◽

Nikodemus Umbu Janga Hauwali ◽

Ahmad Rosikhin ◽

Euis Sustini ◽

Fatimah Arofiati Noor ◽

...

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Bond Order ◽

Interatomic Potential ◽

Interatomic Potentials ◽

Many Body ◽

Range Interaction ◽

Dynamics Simulations ◽

Interaction Approach ◽

Many Body Interactions

AbstractIn this work, we present the bond order redefinition needed to reduce the inherent noise in order to enhance the accuracy of molecular dynamics simulations. We propose defining the bond order as a fraction of energy distribution. It happens due to the character of the material in nature, which tries to maintain its environment. To show the necessity, we developed a factory empirical interatomic potential (FEIP) for carbon that implements the redefinition with a short-range interaction approach. FEIP has been shown to enhance the accuracy of the calculation of lattice constants, cohesive energy, elastic properties, and phonons compared to experimental data, and can even be compared to other potentials with the long-range interaction approach. The enhancements due to FEIP can reduce the inherent noise, then provide a better prediction of the energy based on the behaviour of the atomic environment. FEIP can also transform simple two-body interactions into many-body interactions, which is useful for enhancing accuracy. Due to implementing the bond order redefinition, FEIP offers faster calculations than other complex interatomic potentials.

Download Full-text

Data-Driven Many-Body Models with Chemical Accuracy for CH4/H2O Mixtures

10.26434/chemrxiv.13013057 ◽

2020 ◽

Author(s):

Marc Riera ◽

Alan Hirales ◽

Raja Ghosh ◽

Francesco Paesani

Keyword(s):

Liquid Phase ◽

Quantitative Description ◽

Liquid Mixtures ◽

Many Body ◽

Energy Functions ◽

Potential Energy Functions ◽

Dynamics Simulations ◽

Body Potential ◽

Small Clusters ◽

Many Body Interactions

<div> <div> <div> <p>Many-body potential energy functions (PEFs) based on the TTM-nrg and MB-nrg theoretical/computational frameworks are developed from coupled cluster reference data for neat methane and mixed methane/water systems. It is shown that that the MB-nrg PEFs achieve subchemical accuracy in the representation of individual many-body effects in small clusters and enables predictive simulations from the gas to the liquid phase. Analysis of structural properties calculated from molecular dynamics simulations of liquid methane and methane/water mixtures using both TTM-nrg and MB-nrg PEFs indicates that, while accounting for polarization effects is important for a correct description of many-body interactions in the liquid phase, an accurate representation of short-range interactions, as provided by the MB-nrg PEFs, is necessary for a quantitative description of the local solvation structure in liquid mixtures. </p> </div> </div> </div>

Download Full-text

Fast (Parallel) Algorithms for Spherical Transforms and Many-Body Interactions with Applications in Electrostratics, Image Processing and Chemistry

10.21236/ada387330 ◽

2001 ◽

Author(s):

S. L. Johnsson ◽

Dragan Mirkovic

Keyword(s):

Image Processing ◽

Parallel Algorithms ◽

Many Body ◽

Spherical Transforms ◽

Many Body Interactions

Download Full-text

Localization and many-body interactions in the quantum Hall effect determined by polarized optical emission

Physical Review B ◽

10.1103/physrevb.44.4006 ◽

1991 ◽

Vol 44 (8) ◽

pp. 4006-4009 ◽

Cited By ~ 41

Author(s):

B. B. Goldberg ◽

D. Heiman ◽

M. Dahl ◽

A. Pinczuk ◽

L. Pfeiffer ◽

...

Keyword(s):

Hall Effect ◽

Quantum Hall Effect ◽

Quantum Hall ◽

Optical Emission ◽

Many Body ◽

Many Body Interactions

Download Full-text

Revealing the many-body interactions and valley-polarization behavior in Re-doped MoS2 monolayers

Applied Physics Letters ◽

10.1063/5.0045916 ◽

2021 ◽

Vol 118 (11) ◽

pp. 113101

Author(s):

Xiaoli Zhu ◽

Siting Ding ◽

Lihui Li ◽

Ying Jiang ◽

Biyuan Zheng ◽

...

Keyword(s):

Many Body ◽

Polarization Behavior ◽

Valley Polarization ◽

Mos2 Monolayers ◽

The Many ◽

Many Body Interactions

Download Full-text

Epidemic growth and Griffiths effects on an emergent network of excited atoms

Nature Communications ◽

10.1038/s41467-020-20333-7 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

T. M. Wintermantel ◽

M. Buchhold ◽

S. Shevate ◽

M. Morgado ◽

Y. Wang ◽

...

Keyword(s):

Complex Systems ◽

Power Laws ◽

Excitation Density ◽

Griffiths Phase ◽

Many Body ◽

Excited Atoms ◽

Equilibrium Dynamics ◽

Many Body Systems ◽

Excitation Number ◽

Non Equilibrium

AbstractWhether it be physical, biological or social processes, complex systems exhibit dynamics that are exceedingly difficult to understand or predict from underlying principles. Here we report a striking correspondence between the excitation dynamics of a laser driven gas of Rydberg atoms and the spreading of diseases, which in turn opens up a controllable platform for studying non-equilibrium dynamics on complex networks. The competition between facilitated excitation and spontaneous decay results in sub-exponential growth of the excitation number, which is empirically observed in real epidemics. Based on this we develop a quantitative microscopic susceptible-infected-susceptible model which links the growth and final excitation density to the dynamics of an emergent heterogeneous network and rare active region effects associated to an extended Griffiths phase. This provides physical insights into the nature of non-equilibrium criticality in driven many-body systems and the mechanisms leading to non-universal power-laws in the dynamics of complex systems.

Download Full-text