Kinetic Theory and Shear Viscosity of Dense Dipolar Hard Sphere Liquids.

Transport properties of dense fluids are fundamentally challenging, because the powerful approaches of equilibrium statistical physics cannot be applied. Polar fluids compound this problem, because the long-range interactions preclude the use of a simple effective diameter approach based solely on hard spheres. Here, we develop a kinetic theory for dipolar hard-sphere fluids that is valid up to high density. We derive a mathematical approximation for the radial distribution function at contact directly from the equation of state, and use it to obtain the shear viscosity. We also perform molecular-dynamics simulations of this system and extract the shear viscosity numerically. The theoretical results compare favorably to the simulations.

Stretching and breaking of PEO nanofibres. A classical force field and ab initio simulation study.

The burgeoning development of nanotechnology is allowing us to construct more and more nano-scale systems in the real world that used to only exist in computer simulations. Among them, nanofibres made of only a few aligned polymeric chains in particular might soon have important roles in nanofabrications as well as in nanomedicine. In this work, we present a broad exploration by computer simulations of elastic and inelastic properties of polyethylene-oxide (PEO) nanofibres under load. We cover the full range from unloaded fibres up to their breaking point, focusing on all features that arise from chain-chain interactions and collective behaviour of the chains. We employ both molecular dynamics (MD) simulations and density functional theory (DF). The classical force field is represented by a minimal reactive force field model, allowing for the breaking of covalent bonds. Density functional (DF) computations provide a benchmark to gauge and validate the empirical force field approach, and offer an intriguing view of the bundle chemical evolution after breaking. Force-field based MD is employed for the systematic investigation of bundles of up to 24 chains, and for a single bundle of 100 chains. Low-temperature results for bundles under moderate loading provide a size-dependent sequence of cross-sections, structures, cohesive energies and elastic properties. A remarkably high Young's modulus on the order of 100 GPa was estimated with DF and MD, explained by the semi-crystalline state of the fibres giving mechanical properties comparable to those of carbon nanotubes and of graphene. Breaking is investigated by simulations with constant strain rate or constant stress. The bundle breaks whenever the potential energy is raised above its metastability range, but also below that limit due to creep activated by thermal fluctuations. A Kramer's-type approximation for the rate of chain breaking is proposed and compared to simulation data.

The Vanishing water/oil interface in the presence of antagonistic salt.

Antagonistic salts are salts that consist of hydrophilic and hydrophobic ions. In a binary mixture of water and an organic solvent, these ions preferentially dissolve into different phases. We investigate the effect of an antagonistic salt, tetraphenylphosphonium chloride PPh4 +Cl-, in a mixture of water and 2,6-lutidine by means of Molecular Dynamics (MD) simulations. For increasing concentrations of the salt, the two-phase region is shrunk and the interfacial tension in reduced, in contrast to what happens when a normal salt is added to such a mixture. The MD simulations allow us to investigate in detail the mechanism behind the reduction of the surface tension. We obtain the ion and composition distributions around the interface and determine the hydrogen bonds in the system and conclude that the addition of salt alters the hydrogen bonding.

Stochastic modelling of tyrosine kinase inhibitor rotation therapy in chronic myeloid leukaemia.

BACKGROUND: Resistance towards targeted cancer treatments caused by single nucleotide variations is a major issue in many malignancies. Currently, there are a number of available drugs for chronic myeloid leukaemia (CML), which are overcome by different sets of mutations. The main aim of this study was to explore if it can be possible to exploit this and create a treatment protocol that outperforms each drug on its own. METHODS: We present a computer program to test different treatment protocols against CML, based on available resistance mutation growth data. The evolution of a relatively stable pool of cancer stem cells is modelled as a stochastic process, with the growth of cells expressing a tumourigenic protein (here, Abl1) and any emerging mutants determined principally by the drugs used in the therapy. RESULTS: There can be some benefit to Bosutinib-Ponatinib rotation therapy even if the mutation status is unknown, whereas Imatinib-Nilotinib rotation is unlikely to improve the outcomes. Furthermore, an interplay between growth inhibition and selection effects generates a non-linear relationship between drug doses and the risk of developing resistance. CONCLUSIONS: Drug rotation therapy might be able to delay the onset of resistance in CML patients without costly ongoing observation of mutation status. Moreover, the simulations give credence to the suggestion that lower drug concentrations may achieve better results following major molecular response in CML.

Interplay of mutations, alternate mechanisms, and treatment breaks in leukaemia: Understanding and implications studied with stochastic models.

Bcr-Abl1 kinase domain mutations are the most prevalent cause of treatment resistance in chronic myeloid leukaemia (CML). Alternate resistance pathways nevertheless exist, and cell line experiments show certain patterns in the gain, and loss, of some of these alternate adaptations. These adaptations have clinical consequences when the tumour develops mechanisms that are beneficial to its growth under treatment, but slow down its growth when not treated. The results of temporarily halting treatment in CML have not been widely discussed in the clinic and there is no robust theoretical model that could suggest when such a pause in therapy can be tolerated. We constructed a dynamic model of how mechanisms such as Bcr-Abl1 overexpression and drug transporter upregulation evolve to produce resistance in cell lines, and investigate its behaviour subject to different treatment schedules, in particular when the treatment is paused ('drug holiday'). Our study results suggest that the presence of additional resistance mechanisms creates an environment which favours mutations that are either preexisting or occur late during treatment. Importantly, the results suggest the existence of tumour drug addiction, where cancer cells become dependent on the drug for (optimal) survival, which could be exploited through a treatment holiday. All simulation code is available at https://github.com/Sandalmoth/dual-adaptation.

Viscosity of liquid mixtures: the Vesovic-Wakeham method for chain molecules.

New expressions for the viscosity of liquid mixtures, consisting of chain-like molecules, are derived by means of Enskog-type analysis. The molecules of the fluid are modelled as chains of equally sized, tangentially joined, and rigid spheres. It is assumed that the collision dynamics in such a fluid can be approximated by instantaneous collisions. We determine the molecular size parameters from the viscosity of each pure species and show how the different effective parameters can be evaluated by extending the Vesovic-Wakeham (VW) method. We propose and implement a number of thermodynamically consistent mixing rules, taking advantage of SAFT-type analysis, in order to develop the VW method for chain molecules. The predictions of the VW-chain model have been compared in the first instance with experimental viscosity data for octane-dodecane and methane-decane mixtures, thus, illustrating that the resulting VW-chain model is capable of accurately representing the viscosity of real liquid mixtures.

Nanoscale friction and wear of a polymer coated with graphene.

Friction and wear of polymers at the nanoscale is a challenging problem due to the complex viscoelastic properties and structure. Using molecular dynamics simulations, we investigate how a graphene sheet on top of the semicrystalline polymer polyvinyl alcohol affects the friction and wear. Our setup is meant to resemble an AFM experiment with a silicon tip. We have used two different graphene sheets, namely an unstrained, flat sheet, and one that has been crumpled before being deposited on the polymer. The graphene protects the top layer of the polymer from wear and reduces the friction. The unstrained flat graphene is stiffer, and we find that it constrains the polymer chains and reduces the indentation depth.

Molecular-Dynamics Simulations of the Emergence of Surface Roughness in a Polymer under Compression.

Roughness of surfaces is both surprisingly ubiquitous on all length scales and extremely relevant practically. The appearance of multi-scale roughness has been linked to avalanches and plastic deformation in metals. However, other, more-complex materials have mechanisms of plasticity that are significantly different from those of metals. We investigated the emergence of roughness in a polymer under compression. We performed molecular-dynamics simulations of a slab of solid polyvinyl alcohol that was compressed bi-axially, and we characterised the evolution of the surface roughness. We found significantly different behaviour than what was previously observed in similar simulations of metals. We investigated the differences and argue that the visco-elasticity of the material plays a crucial role.

Dynamics of collective action to conserve a large common-pool resource.

A pressing challenge for coming decades is sustainable and just management of large-scale common-pool resources including the atmosphere, biodiversity and public services. This poses a difficult collective action problem because such resources may not show signs that usage restraint is needed until tragedy is almost inevitable. To solve this problem, a sufficient level of cooperation with a pro-conservation behavioural norm must be achieved, within the prevailing sociopolitical environment, in time for the action taken to be effective. Here we investigate the transient dynamics of behavioural change in an agent-based model on structured networks that are also exposed to a global external influence. We find that polarisation emerges naturally, even without bounded confidence, but that for rationally motivated agents, it is temporary. The speed of convergence to a final consensus is controlled by the rate at which the polarised clusters are dissolved. This depends strongly on the combination of external influences and the network topology. Both high connectivity and a favourable environment are needed to rapidly obtain final consensus.

Understanding the friction of atomically thin layered materials.

Friction is a ubiquitous phenomenon that greatly affects our everyday lives and is responsible for large amounts of energy loss in industrialised societies. Layered materials such as graphene have interesting frictional properties and are often used as (additives to) lubricants to reduce friction and protect against wear. Experimental Atomic Force Microscopy studies and detailed simulations have shown a number of intriguing effects such as frictional strengthening and dependence of friction on the number of layers covering a surface. Here, we propose a simple, fundamental, model for friction on thin sheets. We use our model to explain a variety of seemingly contradictory experimental as well as numerical results. This model can serve as a basis for understanding friction on thin sheets, and opens up new possibilities for ultimately controlling their friction and wear protection.

Entropy Production beyond the Thermodynamic Limit from Single-Molecule Stretching Simulations.

Single-molecular systems are a test bed to analyze to what extent thermodynamics applies when the size of the system is drastically reduced. Isometric and isotensional single-molecule stretching experiments and their theoretical interpretations have shown the lack of a thermodynamic limit at those scales and the nonequivalence between their corresponding statistical ensembles. This disparity between thermodynamic results obtained in both experimental protocols can also be observed in entropy production, as previous theoretical results have shown. In this work, we present results from molecular dynamics simulations of stretching of a typical polymer, polyethylene-oxide, where this framework is applied to obtain friction coefficients associated with stretching at the two different statistical ensembles for two different system sizes, from which the entropy production follows. In the smallest system, they are different up to a factor of 2, and for the bigger system, the difference is smaller, as predicted. In this way, we provide numerical evidence that a thermodynamic description is still meaningful for the case of single-molecule stretching.

A Legendre-Fenchel Transform for Molecular Stretching Energies.

Single-molecular polymers can be used to analyze to what extent thermodynamics applies when the size of the system is drastically reduced. We have recently verified using molecular-dynamics simulations that isometric and isotensional stretching of a small polymer result in Helmholtz and Gibbs stretching energies, which are not related to a Legendre transform, as they are for sufficiently long polymers. This disparity has also been observed experimentally. Using molecular dynamics simulations of polyethylene-oxide, we document for the first time that the Helmholtz and Gibbs stretching energies can be related by a Legendre-Fenchel transform. This opens up a possibility to apply this transform to other systems which are small in Hill's sense.

Relating chaos to deterministic diffusion of a molecule adsorbed on a surface.

Chaotic internal degrees of freedom of a molecule can act as noise and affect the diffusion of the molecule on a substrate. A separation of timescales between the fast internal dynamics and the slow motion of the centre of mass on the substrate makes it possible to directly link chaos to diffusion. We discuss the conditions under which this is possible, and show that in simple atomistic models with pair-wise harmonic potentials, strong chaos can arise through the geometry. Using molecular dynamics simulations, we demonstrate that a realistic model of benzene is indeed chaotic, and that the internal chaos affects the diffusion on a graphite substrate.

A kinetic theory description of the viscosity of dense fluids consisting of chain molecules.

An expression for the viscosity of a dense fluid is presented that includes the effect of molecular shape. The molecules of the fluid are approximated by chains of equal-sized, tangentially jointed, rigid spheres. It is assumed that the collision dynamics in such a fluid can be approximated by instantaneous collisions between two rigid spheres belonging to different chains. The approach is thus analogous to that of Enskog for a fluid consisting of rigid spheres. The description is developed in terms of two molecular parameters, the diameter sigma of the spherical segment and the chain length (number of segments) m. It is demonstrated that an analysis of viscosity data of a particular pure fluid alone cannot be used to obtain independently effective values of both sigma and m. Nevertheless, the chain lengths of n-alkanes are determined by assuming that the diameter of each rigid sphere making up the chain can be represented by the diameter of a methane molecule. The effective chain lengths of n-alkanes are found to increase linearly with the number C of carbon atoms present. The dependence can be approximated by a simple relationship m=1+(C-1)3. The same relationship was reported within the context of a statistical associating fluid theory equation of state treatment of the fluid, indicating that both the equilibrium thermodynamic properties and viscosity yield the same value for the chain lengths of n-alkanes.

Atomic-scale sliding friction on a contaminated surface.

Using non-equilibrium molecular dynamic simulations, we investigate the effect of adsorbates on nanoscopic friction. We find that the interplay between different channels of energy dissipation at the frictional interface may lead to non-monotonic dependence of the friction force on the adsorbate surface coverage and to strongly nonlinear variation of friction with normal load (non-Amontons' behavior). Our simulations suggest that the key parameter controlling the variation of friction force with the normal load, surface coverage and temperature is the time-averaged number of adsorbates confined between the tip and the substrate. Three different regimes of temperature dependence of friction in the presence of adsorbates are predicted. Our findings point on new ways to control friction on contaminated surfaces.

Vertical chaos and horizontal diffusion in the bouncing-ball billiard.

The bouncing-ball billiard is a low-dimensional system with which transport properties of real physical systems can be studied theoretically. We study the bouncing-ball billiard with nonconvex scatterers and small slopes. We show that between the horizontal and vertical motion there is a separation of time scales, which is controlled by the slope of the billiard. We apply the theory of time-scale separation developed by Kantz Physica D 187, 200 (2004). If the vertical motion is chaotic, the horizontal motion is diffusive, but if the vertical motion is (quasi)periodic, there is no diffusion. We confirm the results with numerical simulations. Hence, the order-chaos transition in the vertical degrees of freedom translates into a localization-delocalization transition for the horizontal motion.