scholarly journals Entropic organization of interphase chromosomes

2009 ◽  
Vol 186 (6) ◽  
pp. 825-834 ◽  
Author(s):  
Peter R. Cook ◽  
Davide Marenduzzo
Keyword(s):  
Monte Carlo ◽  
Monte Carlo Simulations ◽  
The Self ◽  
Self Organization ◽  
Centromeric Heterochromatin ◽  
Flexible Polymers

Chromosomes are not distributed randomly in nuclei. Appropriate positioning can activate (or repress) genes by bringing them closer to active (or inactive) compartments like euchromatin (or heterochromatin), and this is usually assumed to be driven by specific local forces (e.g., involving H bonds between nucleosomes or between nucleosomes and the lamina). Using Monte Carlo simulations, we demonstrate that nonspecific (entropic) forces acting alone are sufficient to position and shape self-avoiding polymers within a confining sphere in the ways seen in nuclei. We suggest that they can drive long flexible polymers (representing gene-rich chromosomes) to the interior, compact/thick ones (and heterochromatin) to the periphery, looped (but not linear) ones into appropriately shaped (ellipsoidal) territories, and polymers with large terminal beads (representing centromeric heterochromatin) into peripheral chromocenters. Flexible polymers tend to intermingle less than others, which is in accord with observations that gene-dense (and so flexible) chromosomes make poor translocation partners. Thus, entropic forces probably participate in the self-organization of chromosomes within nuclei.

Kinetic Monte Carlo Simulations of Self-organization of Ge Islands on Si(001)

2021 ◽  
Author(s):  
Paramita Ghosh ◽  
Nidhi Gupta ◽  
Monika Dhankhar ◽  
Madhav Ranganathan
Keyword(s):  
Monte Carlo Simulation ◽  
Monte Carlo ◽  
Monte Carlo Simulations ◽  
Kinetic Monte Carlo ◽  
The Self ◽  
Self Organization ◽  
Kinetic Monte Carlo Simulation ◽  
Kinetic Monte Carlo Simulations

The self-organization of germanium islands on a silicon (001) substrate is studied using a lattice--based kinetic Monte Carlo simulation. These islands form spontaneously via Stranski-Krastanov mode during growth. The interplay...

Self-assembly of AB diblock copolymer solutions confined in cylindrical nanopores

2017 ◽  
Vol 1 (3) ◽  
pp. 487-494 ◽  
Author(s):  
Yuping Sheng ◽  
Yutian Zhu ◽  
Wei Jiang ◽  
Zeyuan Dong
Keyword(s):  
Monte Carlo ◽  
Monte Carlo Simulations ◽  
Diblock Copolymer ◽  
Self Assembly ◽  
The Self

The self-assembly of AB diblock copolymer solutions confined in a cylindrical nanopore is investigated systematically via Monte Carlo simulations.

Formation of embedded Co nanostructures in Cu(001) surface under electromigration

2020 ◽  
pp. 2150090
Author(s):  
S. V. Kolesnikov ◽  
A. L. Klavsyuk ◽  
A. M. Saletsky
Keyword(s):  
Monte Carlo ◽  
Current Density ◽  
Kinetic Monte Carlo ◽  
The Self ◽  
Atomic Scale ◽  
Self Organization ◽  
Simulation Results ◽  
Self Learning

Formation of embedded Co nanostructures in Cu(001) surface under electromigration is investigated on the atomic scale by performing self-learning kinetic Monte Carlo (kMC) simulations. The analysis of simulation results reveals the following important result. The electromigration of vacancies does not influence on the self-organization of Co nanostructures in the first layer of Cu(001) surface at all values of current density, which can be achieved in experiments.

Structural phases of adsorption for flexible polymers on nanocylinder surfaces

2015 ◽  
Vol 17 (45) ◽  
pp. 30702-30711 ◽  
Author(s):  
Jonathan Gross ◽  
Thomas Vogel ◽  
Michael Bachmann
Keyword(s):  
Monte Carlo ◽  
Monte Carlo Simulations ◽  
Flexible Polymers ◽  
Polymer Model ◽  
Thermodynamic Behavior ◽  
Elastic Polymer

Using Monte Carlo simulations, the thermodynamic behavior of a flexible elastic polymer model in the vicinity of an attractive nanocylinder is investigated. We systematically identify structural phases for varying nanocylinder radii and materials as a functions of temperature and construct hyperphase diagrams.

scholarly journals CATASTROPHIC SENESCENCE OF THE PACIFIC SALMON WITHOUT MUTATION-ACCUMULATION

2001 ◽  
Vol 12 (03) ◽  
pp. 319-323 ◽  
Author(s):  
HILDEGARD MEYER-ORTMANNS
Keyword(s):  
Monte Carlo ◽  
Population Dynamics ◽  
Monte Carlo Simulations ◽  
Pacific Salmon ◽  
Mutation Accumulation ◽  
Self Organization ◽  
Aging Model ◽  
The Pacific ◽  
First Reproduction ◽  
Age Of Death

We derive catastrophic senescence of the Pacific salmon from an aging model which was recently proposed by Stauffer. The model is based on the postulates of a minimum reproduction age and a maximal genetic lifespan. It allows for self-organization of a typical age of first reproduction and a typical age of death. Our Monte Carlo simulations of the population dynamics show that the model leads to catastrophic senescence for semelparous reproduction as it occurs in the case of salmon, to a more gradually increase of senescence for iteroparous reproduction.

Self-organization process in crystalline PbTe/CdTe multilayer structures: Experiment and Monte Carlo simulations

2018 ◽  
Vol 747 ◽  
pp. 809-814 ◽  
Author(s):  
Marcin Mińkowski ◽  
Magdalena A. Załuska–Kotur ◽  
Sławomir Kret ◽  
Sergij Chusnutdinow ◽  
Steffen Schreyeck ◽  
...  
Keyword(s):  
Monte Carlo ◽  
Monte Carlo Simulations ◽  
Self Organization ◽  
Multilayer Structures ◽  
Organization Process

Anomalous Kinetics of the Trapping Reaction in One Dimension Under Steady State Conditions

1995 ◽  
Vol 407 ◽  
Author(s):  
Anna L. Lin ◽  
Raoul Kopelman
Keyword(s):  
Monte Carlo ◽  
Steady State ◽  
Monte Carlo Simulations ◽  
Reaction Rate ◽  
Particle Density ◽  
Self Organization ◽  
One Dimension ◽  
Algebraic Decay ◽  
Kinetic Rate ◽  
Kinetics Of

ABSTRACTWe study the A + B→B trapping reaction under steady state conditions for the case in which both A particles and traps(B) are mobile. Using Monte Carlo simulations, we follow the kinetic rate law in one dimension. Anomalies arise due to self-organization of the A particles, which results in a slower steady state reaction rate than is predicted classically. We find a partial order of reaction with respect to trap density of X = 2, and an overall order for the reaction of Z = 3.2. These results are in agreement with other works which predict an exponential rather than an algebraic decay law with respect to the A particle density.

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