scholarly journals Size-Dependent Properties of Magnetosensitive Polymersomes: Computer Modelling

Sensors ◽  
2019 ◽  
Vol 19 (23) ◽  
pp. 5266
Author(s):  
Aleksandr Ryzhkov ◽  
Yuriy Raikher
Keyword(s):  
Material Parameter ◽  
Computer Modelling ◽  
Single Cells ◽  
A Priori ◽  
Amphiphilic Polymer ◽  
Dynamics Simulation ◽  
Strain Response ◽  
Qualitative Explanation ◽  
Size Dependent ◽  
Nanoscale Object

Magnetosensitive polymersomes, which are amphiphilic polymer capsules whose membranes are filled with magnetic nanoparticles, are prospective objects for drug delivery and manipulations with single cells. A molecular dynamics simulation model that is able to render a detailed account on the structure and shape response of a polymersome to an external magnetic field is used to study a dimensional effect: the dependence of the field-induced deformation on the size of this nanoscale object. It is shown that in the material parameter range that resembles realistic conditions, the strain response of smaller polymersomes, against a priori expectations, exceeds that of larger ones. A qualitative explanation for this behavior is proposed.

Size-dependent cuboctahedron-icosahedron transformations of Co-based bimetallic by molecular dynamics simulation

2018 ◽  
Vol 232 ◽  
pp. 8-10 ◽  
Author(s):  
Yang Gao ◽  
Guojian Li ◽  
Yongjun Piao ◽  
Shiying Liu ◽  
Shan Liu ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Dynamics Simulation ◽  
Size Dependent

scholarly journals Metabolic cost of rapid adaptation of single yeast cells

2020 ◽  
Vol 117 (20) ◽  
pp. 10660-10666 ◽  
Author(s):  
Gabrielle Woronoff ◽  
Philippe Nghe ◽  
Jean Baudry ◽  
Laurent Boitard ◽  
Erez Braun ◽  
...  
Keyword(s):  
Cell Metabolism ◽  
Single Cells ◽  
A Priori ◽  
Metabolic Cost ◽  
Microfluidic System ◽  
Cellular Reprogramming ◽  
Yeast Cells ◽  
Rapid Adaptation ◽  
Metabolic Coupling ◽  
Induced Changes

Cells can rapidly adapt to changing environments through nongenetic processes; however, the metabolic cost of such adaptation has never been considered. Here we demonstrate metabolic coupling in a remarkable, rapid adaptation process (1 in 1,000 cells adapt per hour) by simultaneously measuring metabolism and division of thousands of individual Saccharomyces cerevisiae cells using a droplet microfluidic system: droplets containing single cells are immobilized in a two-dimensional (2D) array, with osmotically induced changes in droplet volume being used to measure cell metabolism, while simultaneously imaging the cells to measure division. Following a severe challenge, most cells, while not dividing, continue to metabolize, displaying a remarkably wide diversity of metabolic trajectories from which adaptation events can be anticipated. Adaptation requires a characteristic amount of energy, indicating that it is an active process. The demonstration that metabolic trajectories predict a priori adaptation events provides evidence of tight energetic coupling between metabolism and regulatory reorganization in adaptation. This process allows S. cerevisiae to adapt on a physiological timescale, but related phenomena may also be important in other processes, such as cellular differentiation, cellular reprogramming, and the emergence of drug resistance in cancer.

Investigation of Indenter-Size-Dependent Nanoplasticity of Silicon by Molecular Dynamics Simulation

2020 ◽  
Vol 2 (9) ◽  
pp. 3039-3047
Author(s):  
Jiapeng Sun ◽  
Bingqian Xu ◽  
Xiaoru Zhuo ◽  
Jing Han ◽  
Zhenquan Yang ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Dynamics Simulation ◽  
Size Dependent

Bayesian reverberation inversion incorporating grain-size dependent regression relations as a priori information

2012 ◽  
Author(s):  
Leif Abrahamsson ◽  
Brodd Leif Andersson ◽  
Sven M. Ivansson ◽  
Jörgen Pihl ◽  
Michael A. Ainslie ◽  
...  
Keyword(s):  
Grain Size ◽  
A Priori ◽  
A Priori Information ◽  
Size Dependent ◽  
Regression Relations ◽  
Priori Information

scholarly journals Volumetric Stress-Strain Analysis of Optohydrodynamically Suspended Biological Cells

2010 ◽  
Vol 133 (1) ◽  
Author(s):  
Sean S. Kohles ◽  
Yu Liang ◽  
Asit K. Saha
Keyword(s):  
Single Cells ◽  
Strain Analysis ◽  
Optical Tweezer ◽  
Three Dimensions ◽  
Shear Stresses ◽  
Strain Response ◽  
Biological Cells ◽  
Two Dimensional ◽  
Stress Strain ◽  
Volumetric Stress

Ongoing investigations are exploring the biomechanical properties of isolated and suspended biological cells in pursuit of understanding single-cell mechanobiology. An optical tweezer with minimal applied laser power has positioned biologic cells at the geometric center of a microfluidic cross-junction, creating a novel optohydrodynamic trap. The resulting fluid flow environment facilitates unique multiaxial loading of single cells with site-specific normal and shear stresses resulting in a physical albeit extensional state. A recent two-dimensional analysis has explored the cytoskeletal strain response due to these fluid-induced stresses [Wilson and Kohles, 2010, “Two-Dimensional Modeling of Nanomechanical Stresses-Strains in Healthy and Diseased Single-Cells During Microfluidic Manipulation,” J Nanotechnol Eng Med, 1(2), p. 021005]. Results described a microfluidic environment having controlled nanometer and piconewton resolution. In this present study, computational fluid dynamics combined with multiphysics modeling has further characterized the applied fluid stress environment and the solid cellular strain response in three dimensions to accompany experimental cell stimulation. A volumetric stress-strain analysis was applied to representative living cell biomechanical data. The presented normal and shear stress surface maps will guide future microfluidic experiments as well as provide a framework for characterizing cytoskeletal structure influencing the stress to strain response.

scholarly journals Asymptotic theory for thin two-ply shells

2020 ◽  
Vol 42 (3) ◽  
pp. 269-282
Author(s):  
David J. Steigmann
Keyword(s):  
Shell Theory ◽  
Asymptotic Theory ◽  
A Priori ◽  
Small Strain ◽  
Asymptotic Model ◽  
Strain Response ◽  
Pure Bending ◽  
Laminated Shells ◽  
Limit Model ◽  
Interfacial Surface

We develop an asymptotic model for the finite-deformation, small-strain response of thin laminated shells composed of two perfectly bonded laminae that exhibit reflection symmetry of the material properties with respect to an interfacial surface. No a priori hypotheses are made concerning the kinematics of deformation. The asymptotic procedure culminates in a generalization of Koiter's well-known shell theory to accommodate the laminated structure, and incorporates a rigorous limit model for pure bending.

scholarly journals Interaction Between Edge Dislocation and Single-Layered Graphene in Aluminum Matrix Investigated by Molecular Dynamics Simulation

2022 ◽  
Vol 2152 (1) ◽  
pp. 012034
Author(s):  
Liu Chen ◽  
Zhencheng Li ◽  
Sai Xu ◽  
Aixue Sha
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Mechanical Response ◽  
Aluminum Matrix ◽  
Shear Plane ◽  
Computational Method ◽  
Dynamics Simulation ◽  
Size Dependent ◽  
Graphene Interface ◽  
Dislocation Movement

Abstract The influence of graphene on dislocation movement and subsequent mechanical response of aluminum is investigated by the computational method of molecular dynamics simulation. A Lennard–Jones potential describing Al-C interaction was obtained through ab initio calculation. It was observed that the 2D graphene could reinforce Al matrix similar to the traditional Orowan mechanism. The Al/graphene interface first attract the gliding dislocation to reduce the system energy, which is unlike the grain boundary to repel gliding dislocations through pile-up mechanism. With the increase of stress, dislocation attracted and trapped at the front of graphene could glide along the interface and finally bypass it through climbing when graphene is orientated out of the shear plane. In addition, the strengthening ability of graphene is size dependent, showing a linear relationship between strength increment and graphene size.

scholarly journals Entangled architecture of rough endoplasmic reticulum (RER) and vacuoles enables topological damping in cytoplasm of an ultra-fast giant cell

2021 ◽  
Author(s):  
Ray Chang ◽  
Manu Prakash
Keyword(s):  
Endoplasmic Reticulum ◽  
Giant Cell ◽  
Rough Endoplasmic Reticulum ◽  
Volume Fraction ◽  
Single Cells ◽  
Cellular Systems ◽  
Confocal Imaging ◽  
Dynamics Simulation ◽  
Cellular Damage ◽  
Novel Association

Cellular systems are known to exhibit some of the fastest movements in the biological world - but little is known as to how single cells can dissipate this energy rapidly and adapt to such large accelerations without sub-cellular damage. To study intracellular adaptations under extreme forces - we investigate Spirostomum ambiguum - a giant cell (1-4mm in length) well known to exhibit ultrafast contractions (50% of body length) within 5 msec with a peak acceleration of 15g. Utilizing transmitted electron microscopy (TEM) and confocal imaging, we discover a novel association of rough endoplasmic reticulum (RER) and vacuoles throughout the cell - forming a contiguous fenestrated cubic membrane architecture that topologically entangles these two organelles. A nearly uniform inter-organelle spacing of 60nm is observed between RER and vacuoles, closely packing the entire cell. Using an overdamped molecular dynamics simulation, we demonstrate how this unique entangled metamaterial responds to external loads by rapidly dissipating energy and helps preserve spatial relationships between organelles. Because this dynamics arises primarily from entanglement of two networks incurring jamming transition at a subcritical volume fraction - we term this phenomena "topological damping". Our findings suggest a new mechanical role of RER-vacuolar meshwork as a metamaterial capable of dissipating energy in an ultra-fast contraction event.

scholarly journals Use of multiple picosecond high-mass molecular dynamics simulations to predict crystallographic B-factors of folded globular proteins

2016 ◽  
Author(s):  
Yuan-Ping Pang
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Molecular Dynamics Simulations ◽  
Root Mean Square ◽  
A Priori ◽  
Model Systems ◽  
Dynamics Simulation ◽  
High Mass ◽  
Mean Square ◽  
Dynamics Simulations

ABSTRACTPredicting crystallographic B-factors of a protein from a conventional molecular dynamics simulation is challenging in part because the B-factors calculated through sampling the atomic positional fluctuations in a picosecond molecular dynamics simulation are unreliable and the sampling of a longer simulation yields overly large root mean square deviations between calculated and experimental B-factors. This article reports improved B-factor prediction achieved by sampling the atomic positional fluctuations in multiple picosecond molecular dynamics simulations that use uniformly increased atomic masses by 100-fold to increase time resolution. Using the third immunoglobulin-binding domain of protein G, bovine pancreatic trypsin inhibitor, ubiquitin, and lysozyme as model systems, the B-factor root mean square deviations (mean ± standard error) of these proteins were 3.1 ± 0.2–9 ± 1 Å2for Cα and 7.3 ± 0.9–9.6 ± 0.2 Å2for Cγ, when the sampling was done, for each of these proteins, over 20 distinct, independent, and 50-picosecond high-mass molecular dynamics simulations using AMBER forcefield FF12MC or FF14SB. These results suggest that sampling the atomic positional fluctuations in multiple picosecond high-mass molecular dynamics simulations may be conducive toa prioriprediction of crystallographic B-factors of a folded globular protein.

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