VISUALIZING SOFT MATTER: MESOSCOPIC SIMULATIONS OF MEMBRANES, VESICLES AND NANOPARTICLES

2007 ◽  
Vol 02 (01) ◽  
pp. 33-55 ◽  
Author(s):  
JULIAN SHILLCOCK ◽  
REINHARD LIPOWSKY
Keyword(s):  
Smart Materials ◽  
Soft Matter ◽  
Dissipative Particle Dynamics ◽  
Lipid Vesicles ◽  
Soft Materials ◽  
Coarse Grained ◽  
Molecular Characteristics ◽  
Dynamics Simulations ◽  
And Behavior ◽  
Mesoscopic Simulations

Biological membranes have properties and behavior that emerge from the propagation of the molecular characteristics of their components across many scales. Artificial smart materials, such as drug delivery vehicles and nanoparticles, often rely on modifying naturally-occurring soft matter, such as polymers and lipid vesicles, so that they possess useful behavior. Mesoscopic simulations allow in silico experiments to be easily and cheaply performed on complex, soft materials requiring as input only the molecular structure of the constituents at a coarse-grained level. They can therefore act as a guide to experimenters prior to performing costly assays. Additionally, mesoscopic simulations provide the only currently feasible window on the length and time scales relevant to important biophysical processes such as vesicle fusion. We describe here recent work using Dissipative Particle Dynamics simulations to explore the structure and behavior of amphiphilic membranes, the fusion of vesicles, and the interactions between rigid nanoparticles and soft surfaces.

scholarly journals A Generic Force Field for Simulating Native Protein Structures Using Dissipative Particle Dynamics

Soft Matter ◽  
2021 ◽  
Author(s):  
Rakesh K Vaiwala ◽  
Ganapathy Ayappa
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Molecular Dynamics Simulations ◽  
Dissipative Particle Dynamics ◽  
Protein Structures ◽  
Particle Dynamics ◽  
Coarse Grained ◽  
Native Protein ◽  
Dynamics Simulations

A coarse-grained force field for molecular dynamics simulations of native structures of proteins in a dissipative particle dynamics (DPD) framework is developed. The parameters for bonded interactions are derived by...

scholarly journals Dynamics of vesicle reshaping and scission under osmotic shocks

2020 ◽  
Author(s):  
Christian Vanhille Campos ◽  
Anđela Šarić
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Time Scales ◽  
Osmotic Shock ◽  
Lipid Vesicles ◽  
Coarse Grained ◽  
Shock Absorption ◽  
Bursting Events ◽  
Dynamics Simulations ◽  
Insight Into

We study the effects of osmotic shocks on lipid vesicles via coarse-grained molecular dynamics simulations by explicitly considering the solute in the system. We find that depending on their nature (hypo- or hypertonic) such shocks can lead to bursting events or engulfing of external material into inner compartments, among other morphology transformations. We characterize the dynamics of these processes and observe a separation of time scales between the osmotic shock absorption and the shape relaxation. Our work consequently provides an insight into the dynamics of compartmentalization in vesicular systems as a result of osmotic shocks, which can be of interest in the context of early proto-cell development and proto-cell compartmentalisation.

scholarly journals Soft Underwater Robot Actuated by Shape-Memory Alloys “JellyRobcib” for Path Tracking through Fuzzy Visual Control

2020 ◽  
Vol 10 (20) ◽  
pp. 7160
Author(s):  
Christyan Cruz Ulloa ◽  
Silvia Terrile ◽  
Antonio Barrientos
Keyword(s):  
Shape Memory ◽  
Soft Materials ◽  
Visual Control ◽  
Computer Assisted ◽  
Soft Robot ◽  
Recent Developments ◽  
Computational Fluid Dynamics Simulations ◽  
Dynamics Simulations ◽  
Autonomous Movement ◽  
And Behavior

Recent developments in bioinspired technologies combined with the advance of intelligent and soft materials have allowed soft robots to replicate the behavior of different animal species. These devices can perform complicated tasks such as reaching or adapting in constrained and unstructured environments. This article proposes a methodology to develop a soft robot called “JellyRobcib” inspired in morphology and behavior by jellyfish, using shape-memory alloy springs as actuators (as bio-muscles). Such actuators can move the jellyfish both vertically and laterally by applying closed-loop fuzzy and visual controls. Additionally, Computer-Assisted Designs and Computational Fluid Dynamics simulations have been carried out to validate the soft robot model. The results show that the robot movements are very close to the morphological behavior of a real jellyfish regarding the curves of displacements, speeds and accelerations, after performing several experiments for autonomous movement: vertical ascent, lateral movements and trajectory tracking, obtaining an accuracy of ±1479 cm and repeatability of 0.944 for lateral movements for fuzzy visual control. Furthermore, thermal measurements were taken throughout a given path, allowing the generation of temperature gradients within the underwater environment for monitoring purposes.

scholarly journals A soft matter computer for soft robots

2019 ◽  
Vol 4 (33) ◽  
pp. eaaw6060 ◽  
Author(s):  
M. Garrad ◽  
G. Soter ◽  
A. T. Conn ◽  
H. Hauser ◽  
J. Rossiter
Keyword(s):  
Smart Materials ◽  
Soft Matter ◽  
Autonomous Robots ◽  
Low Cost ◽  
Input Parameter ◽  
Soft Materials ◽  
Soft Robots ◽  
Stimulus Response ◽  
Bending Actuator ◽  
Two Degree Of Freedom

Despite the growing interest in soft robotics, little attention has been paid to the development of soft matter computational mechanisms. Embedding computation directly into soft materials is not only necessary for the next generation of fully soft robots but also for smart materials to move beyond stimulus-response relationships and toward the intelligent behaviors seen in biological systems. This article describes soft matter computers (SMCs), low-cost, and easily fabricated computational mechanisms for soft robots. The building block of an SMC is a conductive fluid receptor (CFR), which maps a fluidic input signal to an electrical output signal via electrodes embedded into a soft tube. SMCs could perform both analog and digital computation. The potential of SMCs is demonstrated by integrating them into three soft robots: (i) a Softworm robot was controlled by an SMC that generated the control signals necessary for three distinct gaits; (ii) a soft gripper was given a set of reflexes that could be programmed by adjusting the parameters of the CFR; and (iii) a two–degree of freedom bending actuator was switched between three distinct behaviors by varying only one input parameter. SMCs are a low-cost way to integrate computation directly into soft materials and an important step toward entirely soft autonomous robots.

A COARSE-GRAINED MODEL OF MONOOLEIN: COMPARISON WITH THE ATOMISTIC MODEL

2009 ◽  
Vol 08 (01n02) ◽  
pp. 169-173
Author(s):  
J. H. KIM ◽  
S. H. CHOI ◽  
D. H. JUNG ◽  
C. S. CHO ◽  
Y. J. CHOI
Keyword(s):  
Molecular Dynamics ◽  
Lipid Bilayer ◽  
Dissipative Particle Dynamics ◽  
Dynamics Simulation ◽  
Coarse Grained ◽  
Atomistic Model ◽  
Coarse Grained Model ◽  
Cosmetic Industry ◽  
Dynamics Simulations ◽  
Potential Parameters

Monoolein (2,3-dihydroxypropyl (Z)-octadec-9-enoate) is one of the monoacylglycerol and has been studied for various applications in food, pharmaceutical, and cosmetic industry. Those applications make use of the phase behavior of monoolein. In order to understand the lipid bilayer phase of monoolein in mesoscale, a coarse-grained model has been built and tested in this work. The monoolein molecule was represented by two hydrophilic heads and six hydrophobic tails. The three water molecules were also represented as one bead. For comparison, the atomistic model has also been used for molecular dynamics simulation on the lipid bilayer phase in isothermal-isobaric (NPT) ensemble. The interaction and bond bending potential parameters for dissipative particle dynamics (DPD) were obtained with molecular dynamics simulations on lipid bilayer in water. And we also obtained the interaction parameters of the coarse-grained model, which agree well with the atomistic model. We compared the simulated phases using the coarse-grained model with using the atomistic model. With these parameters, we successfully reproduced the lamella phase of monoolein in DPD simulations.

MORPHOLOGICAL PROPERTIES OF PYRROLE AND PHENYLENE ROD–COIL DIBLOCK COPOLYMERS BY DISSIPATIVE PARTICLE DYNAMICS

2013 ◽  
Vol 12 (01) ◽  
pp. 1250100 ◽  
Author(s):  
EROL YILDIRIM ◽  
MINE YURTSEVER
Keyword(s):  
Diblock Copolymers ◽  
Dissipative Particle Dynamics ◽  
Atomic Charge ◽  
Simulation Method ◽  
Particle Dynamics ◽  
Industrial Applications ◽  
Coarse Grained ◽  
Morphological Properties ◽  
Dynamics Simulations ◽  
Phase Behaviors

Poly (para-phenylene)s (PPP) and polypyrroles (PPy) are important members of the conducting polymers. Rod–coil type diblock copolymers formed by coupling of PPP and PPy rigid blocks with polycaprolactone (PCL), polystyrene (PS) and polymethylmethacrylate (PMMA) coil blocks were modeled and morphological properties have been studied by a coarse grained simulation method at the mesoscale. Geometry optimizations and the atomic charge calculations were done quantum mechanically to obtain the input parameters for the mesoscale dynamics simulations. The accurate mixing energies and the Flory–Huggins interaction parameters between the monomers of polymers were calculated and used to study the phase behaviors and the morphologies of the copolymers as a function of type and weight percentages of the blocks by Dissipative Particle Dynamics (DPD) simulations. We showed that the methodology employed took into account not only the interaction parameter and chain length of the blocks but also the chemical structure of the polymers and it could be used to produce the phase diagram of the copolymers which has importance for the industrial applications of such materials. Among the studied copolymers, the most suitable one for thin layer applications was predicted to be PPP–b–PCL in which PPP forms lamellar and cylindrical phases in the PCL matrix if amount of PPP rod block is below 50 wt%.

scholarly journals Generic, phenomenological, on-the-fly renormalized repulsion model for self-limited organization of terminal supraparticle assemblies

2015 ◽  
Vol 112 (25) ◽  
pp. E3161-E3168 ◽  
Author(s):  
Trung Dac Nguyen ◽  
Benjamin A. Schultz ◽  
Nicholas A. Kotov ◽  
Sharon C. Glotzer
Keyword(s):  
Soft Matter ◽  
Dimensionless Parameter ◽  
Shell Morphology ◽  
Coarse Grained ◽  
Promising Candidate ◽  
Coarse Grained Model ◽  
Colloidal Aggregates ◽  
Virus Capsids ◽  
Dynamics Simulations ◽  
Potential Use

Self-limited, or terminal, supraparticles have long received great interest because of their abundance in biological systems (DNA bundles and virus capsids) and their potential use in a host of applications ranging from photonics and catalysis to encapsulation for drug delivery. Moreover, soft, uniform colloidal aggregates are a promising candidate for quasicrystal and other hierarchical assemblies. In this work, we present a generic coarse-grained model that captures the formation of self-limited assemblies observed in various soft-matter systems including nanoparticles, colloids, and polyelectrolytes. Using molecular dynamics simulations, we demonstrate that the assembly process is self-limited when the repulsion between the particles is renormalized to balance their attraction during aggregation. The uniform finite-sized aggregates are further shown to be thermodynamically stable and tunable with a single dimensionless parameter. We find large aggregates self-organize internally into a core–shell morphology and exhibit anomalous uniformity when the constituent nanoparticles have a polydisperse size distribution.

Research progress of field-induced soft smart materials

2018 ◽  
Vol 32 (18) ◽  
pp. 1840010 ◽  
Author(s):  
Han Wu ◽  
Zhi Chao Xu ◽  
Jin Bo Wu ◽  
Wei Jia Wen
Keyword(s):  
Magnetic Field ◽  
Smart Materials ◽  
Soft Matter ◽  
Soft Materials ◽  
Magnetorheological Fluid ◽  
Electrorheological Fluid ◽  
Research Area ◽  
Research Progress ◽  
Polymer Gel ◽  
Field Temperature

The field-induced soft smart materials are a kind of soft matter whose macroscopic properties (mechanical, or optical) can be significantly and actively controlled and manipulated by external fields such as magnetic field, electric field, temperature or light. In this paper, we briefly review the research and application progress of the field-induced soft smart materials in recent years and discuss the development problems and trend in this research area. In particular, we focus on three typical field-induced soft materials of smart materials: magnetorheological fluid, electrorheological fluid, and temperature and light sensitive polymer gel.

Resolution Effects in Dissipative Particle Dynamics Simulations

1998 ◽  
Vol 09 (08) ◽  
pp. 1307-1318 ◽  
Author(s):  
Edo S. Boek ◽  
Paul Van Der Schoot
Keyword(s):  
Dissipative Particle Dynamics ◽  
Finite Size ◽  
Coarse Graining ◽  
System Size ◽  
Particle Dynamics ◽  
Coarse Grained ◽  
Fluid Filtration ◽  
Colloidal Spheres ◽  
Effective Attraction ◽  
Dynamics Simulations

Dissipative Particle Dynamics (DPD) simulations were performed to investigate resolution or "coarse graining" effects on the simulation results. Fluid flow through a periodic array of spheres has been studied as a model for fluid filtration into a porous medium. In our model system, it appears that quantitatively correct results for the dimensionless drag can be obtained for relatively small system sizes. For higher solid volume fractions, it is necessary to increase the system size to avoid finite size and resolution effects. Simulations of colloidal spheres suspended in a DPD fluid show effective attraction between the large colloid particles, causing depletion aggregation. This effect may be expected as a consequence of the coarse-grained nature of the DPD fluid. By imposing a steady shear rate the aggregation can be suppressed. The results show that for dilute suspensions, the Brownian noise in the particle interactions causes an effective colloid polydispersity, which suppresses aggregation effects.

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