Density functional theory for colloidal mixtures of hard platelets, rods, and spheres

A geometry-based density functional theory is presented for mixtures of hard spheres, hard needles and hard platelets; both the needles and the platelets are taken to be of vanishing thickness. Geometrical weight functions that are characteristic for each species are given and it is shown how convolutions of pairs of weight functions recover each Mayer bond of the ternary mixture and hence ensure the correct second virial expansion of the excess free energy functional. The case of sphere-platelet overlap relies on the same approximation as does Rosenfeld's functional for strictly two-dimensional hard disks. We explicitly control contributions to the excess free energy that are of third order in density. Analytic expressions relevant for the application of the theory to states with planar translational and cylindrical rotational symmetry, e.g. to describe behavior at planar smooth walls, are given. For binary sphere-platelet mixtures, in the appropriate limit of small platelet densities, the theory differs from that used in a recent treatment [L. Harnau and S. Dietrich, Phys. Rev. E 71, 011504 (2004)]. As a test case of our approach we consider the isotropic-nematic bulk transition of pure hard platelets, which we find to be weakly first order, with values for the coexistence densities and the nematic order parameter that compare well with simulation results.Comment: 39 pages, 8 figure

The Asakura-Oosawa model in the protein limit: the role of many-body interactions

We study the Asakura-Oosawa model in the "protein limit", where the penetrable sphere radius $R_{AO}$ is much greater than the hard sphere radius $R_c$. The phase behaviour and structure calculated with a full many-body treatment show important qualitative differences when compared to a description based on pair potentials alone. The overall effect of the many-body interactions is repulsive.Comment: 9 pages and 11 figures, submitted to J. Phys.: Condensed Matter, special issue "Effective many-body interactions and correlations in soft matter

Coarse-graining polymers as soft colloids

We show how to coarse grain polymers in a good solvent as single particles, interacting with density-independent or density-dependent interactions. These interactions can be between the centres of mass, the mid-points or end-points of the polymers. We also show how to extend these methods to polymers in poor solvents and mixtures of polymers. Treating polymers as soft colloids can greatly speed up the simulation of complex many-polymer systems, including polymer-colloid mixtures.Comment: to appear in Physica A, special STATPHYS 2001 edition. Content of invited talk by AA

The opposing effects of isotropic and anisotropic attraction on association kinetics of proteins and colloids

The association and dissociation of particles via specific anisotropic interactions is a fundamental process, both in biology (proteins) and in soft matter (colloidal patchy particles). The presence of alternative binding sites can lead to multiple productive states and also to non-productive “decoy” or intermediate states. Besides anisotropic interactions, particles can experience non-specific isotropic interactions. We employ single replica transition interface sampling to investigate how adding a non-productive binding site or a nonspecific isotropic interaction alters the dimerization kinetics of a generic patchy particle model. The addition of a decoy binding site reduces the association rate constant, independent of the site’s position, while adding an isotropic interaction increases it due to an increased rebinding probability. Surprisingly, the association kinetics becomes non-monotonic for a tetramer complex formed by multivalent patchy particles. While seemingly identical to twoparticle binding with a decoy state, the cooperativity of binding multiple particles leads to a kinetic optimum. Our results are relevant for the understanding and modeling of biochemical networks and self-assembly processes. Published by AIP Publishing. https://doi.org/10.1063/1.500648

Molecular Free Energies, Rates, and Mechanisms from Data-Efficient Path Sampling Simulations

Molecular dynamics is a powerful tool for studying the thermodynamics and kinetics of complex molecular events. However, these simulations can rarely sample the required time scales in practice. Transition path sampling overcomes this limitation by collecting unbiased trajectories and capturing the relevant events. Moreover, the integration of machine learning can boost the sampling while simultaneously learning a quantitative representation of the mechanism. Still, the resulting trajectories are by construction non-Boltzmann-distributed, preventing the calculation of free energies and rates. We developed an algorithm to approximate the equilibrium path ensemble from machine-learning-guided path sampling data. At the same time, our algorithm provides efficient sampling, mechanism, free energy, and rates of rare molecular events at a very moderate computational cost. We tested the method on the folding of the mini-protein chignolin. Our algorithm is straightforward and data-efficient, opening the door to applications in many challenging molecular systems

Density functional theory and demixing of binary hard rod-polymer mixtures

A density functional theory for a mixture of hard rods and polymers modeled as chains built of hard tangent spheres is proposed by combining the functional due to Yu and Wu for the polymer mixtures [J. Chem. Phys. {\bf 117}, 2368 (2002)] with the Schmidt's functional [Phys. Rev. E {\bf 63}, 50201 (2001)] for rod-sphere mixtures. As a simple application of the functional, the demixing transition into polymer-rich and rod-rich phases is examined. When the chain length increases, the phase boundary broadens and the critical packing fraction decreases. The shift of the critical point of a demixing transition is most noticeable for short chains.Comment: 4 pages,2 figures, in press, PR

Statics and dynamics of free and hydrogen-bonded OH groups at the air/water interface

We use classical atomistic molecular dynamics simulations of two water models (SPC/E and TIP4P/2005) to investigate the orientation and reorientation dynamics of two subpopulations of OH groups belonging to water molecules at the air/water interface at 300 K: those OH groups that donate a hydrogen bond (called “bonded”) and those that do not (called “free”). Free interfacial OH groups reorient in two distinct regimes: a fast regime from 0 to 1 ps and a slow regime thereafter. Qualitatively similar behavior was reported by others for free OH groups near extended hydrophobic surfaces. In contrast, the net reorientation of bonded OH groups occurs at a rate similar to that of bulk water. This similarity in reorientation rate results from compensation of two effects: decreasing frequency of hydrogen-bond breaking/formation (i.e., hydrogen-bond exchange) and faster rotation of intact hydrogen bonds. Both changes result from the decrease in density at the air/water interface relative to the bulk. Interestingly, because of the presence of capillary waves, the slowdown of hydrogen-bond exchange is signiffcantly smaller than that reported for water near extended hydrophobic surfaces, but it is almost identical to that reported for water near small hydrophobic solutes. In this sense water at the air/water interface has characteristics of water of hydration of both small and extended hydrophobic solutes.SARA Computing and Networking Services (www.sara.nl)Nederlandse Organisatie voor Wetenschappelijk Onderzoe

Relating Teaching Qualifications and Basic Need Satisfaction in Medical Teaching

Contains fulltext : 182164.pdf (publisher's version ) (Open Access)INTRODUCTION: Teaching Qualifications (TQs) have been implemented in University Medical Centers, but their relation to teachers’ motivation for medical teaching is unknown. Because teacher motivation influences important outcomes, it is crucial to study how TQs are related to promoting teacher motivation, by fulfilling the basic needs of feeling autonomous, competent, and related towards medical teaching. AIMS: To explore relations between TQs and feelings of autonomy, competence, and relatedness towards medical teaching. METHODS: An online questionnaire was used to collect data about teaching at a university hospital. We measured feelings of autonomy, competence, and relatedness towards medical teaching using the Teaching-related Basic Need Satisfaction scale (T-BNS). We applied multivariate regression analysis to examine relations between TQs and basic need satisfaction in teaching. RESULTS: A total of 767 medical teachers participated. TQs appear to be related to feeling competent in teaching. Higher TQ levels are not related to higher feelings of autonomy, competence, and relatedness towards medical teaching. CONCLUSIONS: The results imply that appealing to non-qualified teachers’ feelings of competence towards medical teaching may stir up their enthusiasm for TQ policy. They also call for robust teaching positions to build teaching experience, preferably as early as possible, and for assessing the importance applicants attach to education in job interviews