462 research outputs found
A theoretical and computational study of the mechanics of biomembranes at multiple scales
Lipid membranes are thin objects that form the main separation structure in cells. They have remarkable mechanical properties; while behaving as a solid shell against bending, they exhibit in-plane fluidity. These two aspects of their mechanics are not only interesting from a physical viewpoint, but also fundamental for their biological function. Indeed, the equilibrium shapes of different organelles in the cell rely on the bending elasticity of lipid membranes. On the other hand, the in-plane fluidity of the membrane is essential in functions such as cell motility, mechano-adaptation, or for the lateral diffusion of proteins and other membrane inclusions. The bending rigidity of membranes can be motivated from microscopic models that account for the stress distribution across the membrane thickness. In particular, the microscopic stress across the membrane is routinely computed from molecular dynamics simulations to investigate how different microscopic features, such as the addition of anesthetics or cholesterol, affect their effective mechanical response. The microscopic stress bridges the gap between the statistical mechanics of a set of point particles, the atoms in a molecular dynamics simulation, and continuum mechanics models. However, we lack an unambiguous definition of the microscopic stress, and different definitions of the microscopic stress suggest different connections between molecular and continuum models. In the first Part of this Thesis, we show that many of the existing definitions of the microscopic stress do not satisfy the most basic balance laws of continuum mechanics, and thus are not physically meaningful. This striking issue has motivated us to propose a new definition of the microscopic stress that complies with these fundamental balance laws. Furthermore, we provide a freely available implementation of our stress definition that can be computed from molecular dynamics simulations (mdstress.org). Our definition of the stress along with our implementation provides a foundation for a meaningful analysis of molecular dynamics simulations from a continuum viewpoint. In addition to lipid membranes, we show the application of our methodology to other important systems, such as defective crystals or fibrous proteins. In the second part of the Thesis, we focus on the continuum modeling of lipid membranes. Because these membranes are continuously brought out-of-equilibrium by biological activity, it is important to go beyond curvature elasticity and describe the internal mechanisms associated with bilayer fluidity. We develop a three-dimensional and non-linear theory and a simulation methodology for the mechanics of lipid membranes, which have been lacking in the field. We base our approach on a general framework for the mechanics of dissipative systems, Onsager's variational principle, and on a careful formulation of the kinematics and balance principles for fluid surfaces. For the simulation of our models, we follow a finite element approach that, however, requires of unconventional dicretization methods due to the non-linear coupling between shape changes and tangent flows on fluid surfaces. Our formulation provides the basis for further investigations of the out-of-equilibrium chemo-mechanics of lipid membranes and other fluid surfaces, such as the cell cortex.Las membranas lipídicas son estructuras delgadas que forman la separación fundamental de las células. Tienen propiedades físicas notables: mientras que se comportan como láminas delgadas sólidas frente a curvatura, presentan fluidez interfacial. Estos dos aspectos de su mecánica son interesantes desde un punto de vista físico e ingenieril, pero además son fundamentales para su función biológica. Las formas de equilibrio de diferentes organelos celulares dependen de la elasticidad frente a curvatura de la membrana lipídica. Por otro lado, la fluidez interfacial es esencial en funciones como la movilidad celular, la adaptación mecánica a deformaciones, o para la difusión lateral de proteínas. La elasticidad frente a curvatura de las membranas lipídicas puede motivarse a través de modelos microscópicos que tienen en cuenta la distribución de esfuerzos a lo largo del espesor de la membrana. En particular, el tensor de esfuerzos microscópico se calcula habitualmente en simulaciones de dinámica molecular a lo largo del espesor de la membrana para investigar cómo diferentes características microscópicas, como la adición de anestésicos o colesterol, afecta la respuesta mecánica efectiva. El tensor de esfuerzos microscópico tiende un puente entre la mecánica estadística de un conjunto de partículas puntuales, los átomos de una simulación de dinámica molecular, y modelos de mecánica de medios continuos. Sin embargo, no disponemos de una definición única del tensor de esfuerzos microscópico, y diferentes definiciones dan lugar a diferentes interpretaciones de la conexión entre modelos moleculares y continuos. En la primera parte de la tesis, mostramos que muchas de las definiciones del tensor de esfuerzos microscópico no satisfacen las leyes más básicas de la mecánica de medios continuos, y por tanto no son físicamente relevantes. Este problema nos ha motivado a proponer una nueva definición del tensor de esfuerzos microscópicos que cumpla las leyes fundamentales de la mecánica de medios continuos por construcción. Además, hemos desarrollado (y puesto a disposición del público libremente) una implementación numérica de nuestra definición del tensor de esfuerzos microscópico que puede calcularse mediante simulaciones de dinámica molecular (mdstress.org). Nuestra definición del tensor de esfuerzos, así como nuestra implementación del mismo, proporcionan una base sólida para el análisis de simulaciones de dinámica molecular desde un punto de vista continuo. Además de membranas lipídicas, mostramos la aplicación de nuestro método en otros sistemas relevantes, como cristales con defectos o proteínas fibrosas. En la segunda parte de esta tesis nos hemos focalizado en el modelado continuo de membranas lipídicas. Ya que estas membranas están constantemente sufriendo actividad biológica que las lleva fuera de equilibrio, es importante tener en cuenta no sólo la elasticidad de curvatura, sino también los grados de libertad internos asociados a la fluidez de la membrana. Para ello, desarrollamos un nuevo marco teórico y computacional general, tridimensional y no-lineal, para la mecánica de membranas lipídicas. Nuestro enfoque se basa en un marco general para la mecánica de sistemas disipativos, el principio variacional de Onsager, y en una formulación cuidadosa de la cinemática y las ecuaciones de balance para superficies fluídas. Para la simulación de nuestros modelos, seguimos una aproximación basada en elementos finitos que, sin embargo, requiere de métodos no convencionales debido al acoplamiento no-lineal entre cambios de forma y los campos de velocidad tangentes en superficies fluídas. Nuestra formulación proporciona la base para futuras investigaciones de la quimiomecánica fuera de equilibrio de membranas lipídicas y otras superficies fluídas, como el cortex celula
Systematic coarse-graining of the dynamics of entangled polymer melts: the road from chemistry to rheology
For optimal processing and design of entangled polymeric materials it is
important to establish a rigorous link between the detailed molecular
composition of the polymer and the viscoelastic properties of the macroscopic
melt. We review current and past computer simulation techniques and critically
assess their ability to provide such a link between chemistry and rheology. We
distinguish between two classes of coarse-graining levels, which we term
coarse-grained molecular dynamics (CGMD) and coarse-grained stochastic dynamics
(CGSD). In CGMD the coarse-grained beads are still relatively hard, thus
automatically preventing bond crossing. This also implies an upper limit on the
number of atoms that can be lumped together and therefore on the longest chain
lengths that can be studied. To reach a higher degree of coarse-graining, in
CGSD many more atoms are lumped together, leading to relatively soft beads. In
that case friction and stochastic forces dominate the interactions, and actions
must be undertaken to prevent bond crossing. We also review alternative methods
that make use of the tube model of polymer dynamics, by obtaining the
entanglement characteristics through a primitive path analysis and by
simulation of a primitive chain network. We finally review super-coarse-grained
methods in which an entire polymer is represented by a single particle, and
comment on ways to include memory effects and transient forces.Comment: Topical review, 31 pages, 10 figure
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Coarse-grained simulations to predict structure and properties of polymer nanocomposites
textPolymer Nanocomposites (PNC) are a new class of materials characterized by their large interfacial areas between the host
polymer and nanofiller. This unique feature, due to the size of the
nanofiller, is understood to be the cause of enhanced
mechanical, electrical, optical, and barrier properties observed of
PNCs, relative to the properties of the unfilled polymer. This
interface can determine the miscibility of the nanofiller in the
polymer, which, in turn, influences the PNC's properties. In addition,
this interface alters the polymer's structure near the surface of the
nanofiller resulting in heterogeneity of local properties that can be
expressed at the macroscopic level.
Considering the polymer-nanoparticle interface significantly
influences PNC properties, it is apparent that some atomistic level of
detail is required to accurately predict the behavior of
PNCs. Though an all-atom simulation of a PNC would be able to
accomplish the latter, it is an impractical approach to pursue even with
the most advanced computational resources currently available.
In this contribution, we develop
(1) an equilibrium coarse-graining method to predict nanoparticle
dispersion in a polymer melt, (2) a dynamic coarse-graining method
to predict rheological properties of polymer-nanoparticle melt
mixtures, and (3) a numerical approach that includes interfacial
layer effects and polymer rigidity when predicting barrier properties
of PNCs.
In addition to the above, we study how particle and polymer
characteristics affect the interfacial layer thickness as well as how
the polymer-nanoparticle interface may influence the entanglement
network in a polymer melt. More specifically, we use a mean-field
theory approach to discern how the concentration of a semiflexible
polymer, its rigidity and the particle's size determine the
interfacial layer thickness, and the scaling laws to describe this
dependency. We also utilize molecular dynamics and simulation
techniques on a model
PNC to determine if the polymer-nanoparticle interaction can influence
the entanglement network of a polymer melt.Chemical Engineerin
Efficient Reactive Brownian Dynamics
We develop a Split Reactive Brownian Dynamics (SRBD) algorithm for particle
simulations of reaction-diffusion systems based on the Doi or volume reactivity
model, in which pairs of particles react with a specified Poisson rate if they
are closer than a chosen reactive distance. In our Doi model, we ensure that
the microscopic reaction rules for various association and disassociation
reactions are consistent with detailed balance (time reversibility) at
thermodynamic equilibrium. The SRBD algorithm uses Strang splitting in time to
separate reaction and diffusion, and solves both the diffusion-only and
reaction-only subproblems exactly, even at high packing densities. To
efficiently process reactions without uncontrolled approximations, SRBD employs
an event-driven algorithm that processes reactions in a time-ordered sequence
over the duration of the time step. A grid of cells with size larger than all
of the reactive distances is used to schedule and process the reactions, but
unlike traditional grid-based methods such as Reaction-Diffusion Master
Equation (RDME) algorithms, the results of SRBD are statistically independent
of the size of the grid used to accelerate the processing of reactions. We use
the SRBD algorithm to compute the effective macroscopic reaction rate for both
reaction- and diffusion-limited irreversible association in three dimensions.
We also study long-time tails in the time correlation functions for reversible
association at thermodynamic equilibrium. Finally, we compare different
particle and continuum methods on a model exhibiting a Turing-like instability
and pattern formation. We find that for models in which particles diffuse off
lattice, such as the Doi model, reactions lead to a spurious enhancement of the
effective diffusion coefficients.Comment: To appear in J. Chem. Phy
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How Water's Properties Are Encoded in Its Molecular Structure and Energies.
How are water's material properties encoded within the structure of the water molecule? This is pertinent to understanding Earth's living systems, its materials, its geochemistry and geophysics, and a broad spectrum of its industrial chemistry. Water has distinctive liquid and solid properties: It is highly cohesive. It has volumetric anomalies-water's solid (ice) floats on its liquid; pressure can melt the solid rather than freezing the liquid; heating can shrink the liquid. It has more solid phases than other materials. Its supercooled liquid has divergent thermodynamic response functions. Its glassy state is neither fragile nor strong. Its component ions-hydroxide and protons-diffuse much faster than other ions. Aqueous solvation of ions or oils entails large entropies and heat capacities. We review how these properties are encoded within water's molecular structure and energies, as understood from theories, simulations, and experiments. Like simpler liquids, water molecules are nearly spherical and interact with each other through van der Waals forces. Unlike simpler liquids, water's orientation-dependent hydrogen bonding leads to open tetrahedral cage-like structuring that contributes to its remarkable volumetric and thermal properties
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