A general formulation of Bead Models applied to flexible fibers and active filaments at low Reynolds number

This contribution provides a general framework to use Lagrange multipliers for the simulation of low Reynolds number fiber dynamics based on Bead Models (BM). This formalism provides an efficient method to account for kinematic constraints. We illustrate, with several examples, to which extent the proposed formulation offers a flexible and versatile framework for the quantitative modeling of flexible fibers deformation and rotation in shear flow, the dynamics of actuated filaments and the propulsion of active swimmers. Furthermore, a new contact model called Gears Model is proposed and successfully tested. It avoids the use of numerical artifices such as repulsive forces between adjacent beads, a source of numerical difficulties in the temporal integration of previous Bead Models.Comment: 41 pages, 15 figure

Computer simulation of liquid crystals

A review is presented of molecular and mesoscopic computer simulations of liquid crystalline systems. Molecular simulation approaches applied to such systems are described and the key findings for bulk phase behaviour are reported. Following this, recently developed lattice Boltzmann (LB) approaches to the mesoscale modelling of nemato-dynamics are reviewed. The article concludes with a discussion of possible areas for future development in this field.</p

Interactive Problem Structuring with ICZM Stakeholders

Integrated Coastal Zone Management (ICZM) is struggling with a lack of science-management integration. Many computer systems, usually known as “decision support systems”, have been developed with the intention to make scientific knowledge about complex systems more accessible for coastal managers. These tools, allowing a multi-disciplinary approach with multi-criteria analyses, are designed for well-defined, structured problems. However, in practice stakeholder consensus on the problem structure is usually lacking. Aim of this paper is to explore the practical opportunities for the new so-called Quasta approach to structure complex problems in a group setting. This approach is based on a combination of Cognitive Mapping and Qualitative Probabilistic Networks. It comprehends a new type of computer system which is quite simple and flexible as well. The tool is tested in two workshops in which various coastal management issues were discussed. Evaluations of these workshops show that (1) this system helps stakeholders to make them aware of causal relationships, (2) it is useful for a qualitative exploration of scenarios, (3) it identifies the quantitative knowledge gaps of the problem being discussed and (4) the threshold for non technicians to use this tool is quite low.Integrated Coastal Zone Management, Problem Structuring, Stakeholder Participation, Cognitive Mapping, Interactive Policy Making

On 4-point correlation functions in simple polymer models

We derive an exact formula for the covariance of cartesian distances in two simple polymer models, the freely-jointed chain and a discrete flexible model with nearest-neighbor interaction. We show that even in the interaction-free case correlations exist as long as the two distances at least partially share the same segments. For the interacting case, we demonstrate that the naive expectation of increasing correlations with increasing interaction strength only holds in a finite range of values. Some suggestions for future single-molecule experiments are made

Ring formation in a statistical associating fluid theory framework

Hydrogen bonds (HB) form, most commonly, between independent molecules (intermolecular HB), leading to the formation of linear or branched chain-like networks, which can extend in open form and can include ring-like networks (closed loops). In addition, hydrogen bonds may involve atoms in different parts of the same molecule (intramolecular HB), on occasion leading to bent X-H...X conformations in smaller molecules (e.g., Schiff bases) where strong steric conditions apply, or from within large macromolecules (polymers [1,2,3,4,5] and proteins [6,7,8]) with little constraint from the covalent bonds otherwise binding the atoms. The formation of HB leads to long-lived molecular aggregates and the macroscopic manifestation of these two types of HB bond can be rather different and striking [9, 10, 11, 12, 13]. The direct result of the formation of hydrogen bonds is the decrease in the availability of the donor/acceptor sites of the chemical groups involved to associate. In the development of equations of state (EOSs) based on Wertheim’s thermodynamic perturbation theory (TPT), including the statistical associating fluid theory (SAFT), the formation of any ring clusters, that are formed by inter- or intramolecular hydrogen bonding, is typically neglected. As a consequence, the applicability of SAFT-like EOSs is limited to systems where the anomalies arising from ring formation are insignificant. Previous attempts to extend the TPT formalism to account for rings have not provided all the answers. The issue is addressed here whereby the TPT treatment is extended to account for ring formation, under the approximation that the appropriate many-body distribution function of the ring aggregate can be expressed as a power of a (pair) radial distribution function in a homogeneous fluid. The theory developed in this thesis constitutes an improvement to the existing theories of association in that it can be used to account for the competition between free monomers, linear-chain, branched-chain, inter- and intramolecular ring aggregates by hydrogen bonding. The theory requires as input the size of rings formed and one extra parameter per ring type to capture the probability associated with the two sites in a chain molecule/aggregate meeting each other. The resulting generic framework is applicable to mixtures with an arbitrary number of association sites and ring types. The newly developed treatment is then compared to the standard framework for reference, to examine the impact of ring formation on the phase equilibria of model systems and to model the solubility of ring-forming statins in simple alcohols. The formation of both inter- and intramolecular rings is favoured by the increase of the association energy, low temperature and low density. For fixed parameters, the formation of rings may result in either the enhancement or the decrease of the solubility of statins, depending on the nature of the solvent.Open Acces

A general formulation of Bead Models applied to flexible fibers and active filaments at low Reynolds number

This contribution provides a general framework to use Lagrange multipliers for the simulation of low Reynolds number fiber dynamics based on Bead Models (BM). This formalism provides an efficient method to account for kinematic constraints. We illustrate, with several examples, to which extent the proposed formulation offers a flexible and versatile framework for the quantitative modeling of flexible fibers deformation and rotation in shear flow, the dynamics of actuated filaments and the propulsion of active swimmers. Furthermore, a new contact model called Gears Model is proposed and successfully tested. It avoids the use of numerical artifices such as repulsive forces between adjacent beads, a source of numerical difficulties in the temporal integration of previous Bead Models

Status and Future Perspectives for Lattice Gauge Theory Calculations to the Exascale and Beyond

In this and a set of companion whitepapers, the USQCD Collaboration lays out a program of science and computing for lattice gauge theory. These whitepapers describe how calculation using lattice QCD (and other gauge theories) can aid the interpretation of ongoing and upcoming experiments in particle and nuclear physics, as well as inspire new ones.Comment: 44 pages. 1 of USQCD whitepapers

First-principles calculation of DNA looping in tethered particle experiments

We calculate the probability of DNA loop formation mediated by regulatory proteins such as Lac repressor (LacI), using a mathematical model of DNA elasticity. Our model is adapted to calculating quantities directly observable in Tethered Particle Motion (TPM) experiments, and it accounts for all the entropic forces present in such experiments. Our model has no free parameters; it characterizes DNA elasticity using information obtained in other kinds of experiments. [...] We show how to compute both the "looping J factor" (or equivalently, the looping free energy) for various DNA construct geometries and LacI concentrations, as well as the detailed probability density function of bead excursions. We also show how to extract the same quantities from recent experimental data on tethered particle motion, and then compare to our model's predictions. [...] Our model successfully reproduces the detailed distributions of bead excursion, including their surprising three-peak structure, without any fit parameters and without invoking any alternative conformation of the LacI tetramer. Indeed, the model qualitatively reproduces the observed dependence of these distributions on tether length (e.g., phasing) and on LacI concentration (titration). However, for short DNA loops (around 95 basepairs) the experiments show more looping than is predicted by the harmonic-elasticity model, echoing other recent experimental results. Because the experiments we study are done in vitro, this anomalously high looping cannot be rationalized as resulting from the presence of DNA-bending proteins or other cellular machinery. We also show that it is unlikely to be the result of a hypothetical "open" conformation of the LacI tetramer.Comment: See the supplement at http://www.physics.upenn.edu/~pcn/Ms/TowlesEtalSuppl.pdf . This revised version accepted for publication at Physical Biolog

Vectorial formalism for analysis and design of polyphase synchronous machines

A vectorial formalism for analysis and design of polyphase synchronous machines without reluctance and saturation effects is described. We prove the equivalence of such a machine with a set of magnetically independent machines, which are electrically and mechanically coupled. Specific problems of polyphase machines can thus be favorably analyzed with this concept. Rules of conception and constraints on electric supply can be deduced. Moreover the vectorial approach, which generalizes the complex phasor method, can also be used to control n-leg Voltage Source Inverters. This methodology is applied to 3-phase and 6- phase synchronous machines

Equation of State Based Slip Spring Model for Entangled Polymer Dynamics

A mesoscopic, mixed particle- and field-based Brownian dynamics methodology for the simulation of entangled polymer melts has been developed. Polymeric beads consist of several Kuhn segments, and their motion is dictated by the Helmholtz energy of the sample, which is a sum of the entropic elasticity of chain strands between beads, slip springs, and nonbonded interactions. The entanglement effect is introduced by the slip springs, which are springs connecting either nonsuccessive beads on the same chain or beads on different polymer chains. The terminal positions of slip springs are altered during the simulation through a kinetic Monte Carlo hopping scheme, with rate-controlled creation/destruction processes for the slip springs at chain ends. The rate constants are consistent with the free energy function employed and satisfy microscopic reversibility at equilibrium. The free energy of nonbonded interactions is derived from an appropriate equation of state, and it is computed as a functional of the local density by passing an orthogonal grid through the simulation box; accounting for it is necessary for reproducing the correct compressibility of the polymeric material. Parameters invoked by the mesoscopic model are derived from experimental volumetric and viscosity data or from atomistic molecular dynamics simulations, establishing a "bottom-up" predictive framework for conducting slip spring simulations of polymeric systems of specific chemistry. The mesoscopic simulation methodology is implemented for the case of cis-1,4-polyisoprene, whose structure, dynamics, thermodynamics, and linear rheology in the melt state are quantitatively predicted and validated without a posteriori fitting the results to experimental measurements.Comment: 80 pages, 17 figure