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Biomedical subjects

Mark O Robbins

Publications and source records attributed to Mark O Robbins.

At least 19 recordsLinked to original sources
PubMed2006

General continuum boundary conditions for miscible binary fluids from molecular dynamics simulations.

Molecular dynamics simulations are used to explore the flow behavior and diffusion of miscible fluids near solid surfaces. The solid produces deviations from bulk fluid behavior that decay over a distance of the order of the fluid correlation length. Atomistic results are mapped onto two types of continuum model: Mesoscopic models that follow this decay and conventional sharp interface boundary conditions for the stress and velocity. The atomistic results, and mesoscopic models derived from them, are consistent with the conventional Marangoni stress boundary condition. However, there are deviations from the conventional Navier boundary condition that states that the slip velocity between wall and fluid is proportional to the strain rate. A general slip boundary condition is derived from the mesoscopic model that contains additional terms associated with the Marangoni stress and diffusion, and is shown to describe the atomistic simulations. The additional terms lead to strong flows when there is a concentration gradient. The potential for using this effect to make a nanomotor or pump is evaluated.

Journal Article↗
PubMed2006

Multiscale modeling of two-dimensional contacts.

A hybrid simulation method is introduced and used to study two-dimensional single-asperity and multi-asperity contacts both quasistatically and dynamically. The method combines an atomistic treatment of the interfacial region with a finite-element method description of subsurface deformations. The dynamics in the two regions are coupled through displacement boundary conditions applied at the outer edges of an overlap region. The two solutions are followed concurrently but with different time resolution. The method is benchmarked against full atomistic simulations. Accurate results are obtained for contact areas, pressures, and static and dynamic friction forces. The time saving depends on the fraction of the system treated atomistically and is already more than a factor of 20 for the relatively small systems considered here.

Journal Article↗
PubMed2006

Contact of single asperities with varying adhesion: comparing continuum mechanics to atomistic simulations.

Atomistic simulations are used to test the equations of continuum contact mechanics in nanometer scale contacts. Nominally spherical tips, made by bending crystals or cutting crystalline or amorphous solids, are pressed into a flat, elastic substrate. The normal displacement, contact radius, stress distribution, friction, and lateral stiffness are examined as a function of load and adhesion. The atomic scale roughness present on any tip made of discrete atoms is shown to have profound effects on the results. Contact areas, local stresses, and the work of adhesion change by factors of 2 to 4, and the friction and lateral stiffness vary by orders of magnitude. The microscopic factors responsible for these changes are discussed. The results are also used to test methods for analyzing experimental data with continuum theory to determine information, such as contact area, that cannot be measured directly in nanometer scale contacts. Even when the data appear to be fit by continuum theory, extracted quantities can differ substantially from their true values.

Journal Article↗
PubMed2006

Resolving singular forces in cavity flow: multiscale modeling from atomic to millimeter scales.

Flow driven by moving a wall that bounds a fluid-filled cavity is a classic example of a multiscale problem. Continuum equations predict that every scale contributes roughly equally to the total force on the moving wall, leading to a logarithmic divergence, and that there is an infinite hierarchy of vortices at the stationary corners. A multiscale approach is developed that retains an atomistic description in key regions. Following the stress over more than six decades in length in systems with characteristic scales of up to millimeters and milliseconds allows us to resolve the singularities and determine the force for the first time. We find a universal dependence on the macroscopic Reynolds number, and large atomistic effects that depend on wall velocity and interactions.

Journal Article↗
PubMed2005

Effect of equilibration on primitive path analyses of entangled polymers.

We use recently developed primitive path analysis (PPA) methods to study the effect of equilibration on entanglement density in model polymeric systems. Values of Ne for two commonly used equilibration methods differ by a factor of 2-4 even though the methods produce similar large-scale chain statistics. We find that local chain stretching in poorly equilibrated samples increases entanglement density. The evolution of Ne with time shows that many entanglements are lost through fast processes such as chain retraction as the local stretching relaxes. Quenching a melt state into a glass has little effect on Ne. Equilibration-dependent differences in short-scale structure affect the craze extension ratio much less than expected from the differences in PPA values of Ne.

Journal Article↗
PubMed2005

Unified description of aging and rate effects in yield of glassy solids.

The competing effects of slow structural relaxations (aging) and deformation at constant strain rate on the shear yield stress tau(y) of simple model glasses are examined using molecular simulations. At long times, aging leads to a logarithmic increase in density and tau(y). The yield stress also rises logarithmically with rate but shows a sharp transition in slope at a rate that decreases with increasing age. We present a simple phenomenological model that includes both intrinsic rate dependence and the change in properties with the total age of the system at yield. As predicted by the model, all data for each temperature collapse onto a universal curve.

Journal Article↗
PubMed2005

The breakdown of continuum models for mechanical contacts.

Forces acting within the area of atomic contact between surfaces play a central role in friction and adhesion. Such forces are traditionally calculated using continuum contact mechanics, which is known to break down as the contact radius approaches atomic dimensions. Yet contact mechanics is being applied at ever smaller lengths, driven by interest in shrinking devices to nanometre scales, creating nanostructured materials with optimized mechanical properties, and understanding the molecular origins of macroscopic friction and adhesion. Here we use molecular simulations to test the limits of contact mechanics under ideal conditions. Our findings indicate that atomic discreteness within the bulk of the solids does not have a significant effect, but that the atomic-scale surface roughness that is always produced by discrete atoms leads to dramatic deviations from continuum theory. Contact areas and stresses may be changed by a factor of two, whereas friction and lateral contact stiffness change by an order of magnitude. These variations are likely to affect continuum predictions for many macroscopic rough surfaces, where studies show that the total contact area is broken up into many separate regions with very small mean radius.

Journal Article↗
PubMed2004

Thermal effects in stretching of Go-like models of titin and secondary structures.

The effect of temperature on mechanical unfolding of proteins is studied using a Go-like model with a realistic contact map and Lennard-Jones contact interactions. The behavior of the I27 domain of titin and its serial repeats is contrasted to that of simple secondary structures. In all cases, thermal fluctuations accelerate the unraveling process, decreasing the unfolding force nearly linearly at low temperatures. However, differences in bonding geometry lead to different sensitivity to temperature and different changes in the unfolding pattern. Due to its special native-state geometry, titin is much more thermally and elastically stable than the secondary structures. At low temperatures, serial repeats of titin show a parallel unfolding of all domains to an intermediate state, followed by serial unfolding of the domains. At high temperatures, all domains unfold simultaneously, and the unfolding distance decreases monotonically with the contact order, that is, the sequence distance between the amino acids that form the native contact.

Computer Simulation↗
PubMed2004

Stretching of homopolymers and contact order.

Mechanical stretching of self-interacting homopolymers is studied through molecular dynamics simulations in which the polymers are pulled with constant speed. At temperatures below the compactification temperature, the force-extension curves show a plateau that corresponds to the situation in which the polymer adopts "ball-string" configurations. The dependence of rupture distances on contact order and the effects of temperature are similar to those found in the case of model proteins. The dependence of behavior on the pulling speed is logarithmic. In the entropic limit, above the compactification temperature, the rupturing of contacts shows a monotonic decrease of extension with the contact order. The attainment of this limit depends on the system size and the pulling speed.

Biopolymers↗
PubMed2004

Effect of inertia and elasticity on stick-slip motion.

A hybrid simulation method is used to study the transition from stick-slip motion to steady sliding as the sliding velocity increases above a critical value v(c). The effects of the geometry, elasticity, and mass M of the sliding object are varied to test competing theories. When the slider has a tapered geometry, v(c) scales as M(-1/2), and the elasticity of the slider is irrelevant. When the slider has a constant columnar cross section, elasticity dominates, and v(c) is independent of mass as M--> infinity. The tapered geometry is more typical of existing measurements, but the columnar geometry could be realized using a nanotube.

Journal Article↗
PubMed2004

Fcc-bcc transition for Yukawa interactions determined by applied strain deformation.

Calculations of the work required to transform between bcc and fcc phases yield a high-precision bcc-fcc transition line for monodisperse point Yukawa (screened-Coulomb) systems. Our results agree qualitatively but not quantitatively with recently published simulations and phenomenological criteria for the bcc-fcc transition. In particular, the bcc-fcc-fluid triple point lies at a higher inverse screening length than previously reported.

Journal Article↗
PubMed2004

Mapping molecular models to continuum theories for partially miscible fluids.

We map molecular dynamics simulations of fluid-fluid interfaces onto mesoscale continuum theories for partially miscible fluids. Unlike most previous work, we examine not only the interface order parameter and density profiles, but also the stress. This allows a complete mapping from the length scales of molecular dynamics simulations onto a mesoscale model suitable for a lattice Boltzmann or other mesoscale simulation method. Typical assumptions of mesoscale models, such as incompressibility, are found to fail at the interface, and this has a significant impact on the surface tension. Spurious velocities, found in a number of discrete models of curved interfaces, are found to be minimized when the parameters of the mesoscopic model are made consistent with molecular dynamics results. An improved mesoscale model is given and demonstrated to produce results consistent with molecular dynamics simulations for interfaces with widths down to near molecular size.

Journal Article↗
PubMed2004

Stretching of proteins in the entropic limit.

Mechanical stretching of six proteins is studied through molecular dynamics simulations. The model is Go-like, with Lennard-Jones interactions at native contacts. Low-temperature unfolding scenarios are remarkably complex and sensitive to small structural changes. Thermal fluctuations reduce the peak forces and the number of metastable states during unfolding. The unfolding pathways also simplify as temperature rises. In the entropic limit, all proteins show a monotonic decrease of the extension where bonds rupture with their separation along the backbone (contact order).

Computer Simulation↗
PubMed2003

Shear yielding of amorphous glassy solids: effect of temperature and strain rate.

We study shear yielding and steady state flow of glassy materials with molecular dynamics simulations of two standard models: amorphous polymers and bidisperse Lennard-Jones glasses. For a fixed strain rate, the maximum shear yield stress and the steady state flow stress in simple shear both drop linearly with increasing temperature. The dependence on strain rate can be described by either a logarithm or a power law added to a constant. In marked contrast to predictions of traditional thermal activation models, the rate dependence is nearly independent of temperature. The relation to more recent models of plastic deformation and glassy rheology is discussed, and the dynamics of particles and stress in small regions is examined in light of these findings.

Journal Article↗
PubMed2003

Growth, microstructure, and failure of crazes in glassy polymers.

We report on an extensive study of craze formation in glassy polymers. Molecular dynamics simulations of a coarse-grained bead-spring model were employed to investigate the molecular level processes during craze nucleation, widening, and breakdown for a wide range of temperature, polymer chain length N, entanglement length N(e), and strength of adhesive interactions between polymer chains. Craze widening proceeds via a fibril-drawing process at constant drawing stress. The extension ratio is determined by the entanglement length, and the characteristic length of stretched chain segments in the polymer craze is N(e)/3. In the craze, tension is mostly carried by the covalent backbone bonds, and the force distribution develops an exponential tail at large tensile forces. The failure mode of crazes changes from disentanglement to scission for N/N(e) approximately 10, and breakdown through scission is governed by large stress fluctuations. The simulations also reveal inconsistencies with previous theoretical models of craze widening, which were based on continuum level hydrodynamics.

Glass↗
PubMed2002

Jamming under tension in polymer crazes.

Molecular dynamics simulations are used to study a unique expanded jammed state. Tension transforms many glassy polymers from a dense glass to a network of fibrils and voids called a craze. Entanglements between polymers and interchain friction jam the system after a fixed increase in volume. As in dense jammed systems, the distribution of forces is exponential, but they are tensile rather than compressive. The broad distribution of forces has important implications for fibril breakdown and the ultimate strength of crazes.

Journal Article↗
PubMed2002

Folding and stretching in a Go-like model of titin.

Mechanical stretching of the I27 domain of titin and of its double and triple repeats are studied through molecular dynamics simulations of a Go-like model with Lennard-Jones contact interactions. We provide a thorough characterization of the system and correlate the sequencing of the folding and unraveling events with each other and with the contact order. The roles of cantilever stiffness and pulling rate are studied. Unraveling of tandem titin structures has a serial nature. The force-displacement curves in this coarse-grained model are similar to those obtained through all atom calculations.

Animals↗