@article{9050, abstract = {Self-propelled particles can exhibit surprising non-equilibrium behaviors, and how they interact with obstacles or boundaries remains an important open problem. Here we show that chemically propelled micro-rods can be captured, with little change in their speed, into close orbits around solid spheres resting on or near a horizontal plane. We show that this interaction between sphere and particle is short-range, occurring even for spheres smaller than the particle length, and for a variety of sphere materials. We consider a simple model, based on lubrication theory, of a force- and torque-free swimmer driven by a surface slip (the phoretic propulsion mechanism) and moving near a solid surface. The model demonstrates capture, or movement towards the surface, and yields speeds independent of distance. This study reveals the crucial aspects of activity–driven interactions of self-propelled particles with passive objects, and brings into question the use of colloidal tracers as probes of active matter.}, author = {Takagi, Daisuke and Palacci, Jérémie A and Braunschweig, Adam B. and Shelley, Michael J. and Zhang, Jun}, issn = {1744-6848}, journal = {Soft Matter}, keywords = {General Chemistry, Condensed Matter Physics}, number = {11}, publisher = {Royal Society of Chemistry }, title = {{Hydrodynamic capture of microswimmers into sphere-bound orbits}}, doi = {10.1039/c3sm52815d}, volume = {10}, year = {2014}, } @article{9166, abstract = {Light-activated self-propelled colloids are synthesized and their active motion is studied using optical microscopy. We propose a versatile route using different photoactive materials, and demonstrate a multiwavelength activation and propulsion. Thanks to the photoelectrochemical properties of two semiconductor materials (α-Fe2O3 and TiO2), a light with an energy higher than the bandgap triggers the reaction of decomposition of hydrogen peroxide and produces a chemical cloud around the particle. It induces a phoretic attraction with neighbouring colloids as well as an osmotic self-propulsion of the particle on the substrate. We use these mechanisms to form colloidal cargos as well as self-propelled particles where the light-activated component is embedded into a dielectric sphere. The particles are self-propelled along a direction otherwise randomized by thermal fluctuations, and exhibit a persistent random walk. For sufficient surface density, the particles spontaneously form ‘living crystals’ which are mobile, break apart and reform. Steering the particle with an external magnetic field, we show that the formation of the dense phase results from the collisions heads-on of the particles. This effect is intrinsically non-equilibrium and a novel principle of organization for systems without detailed balance. Engineering families of particles self-propelled by different wavelength demonstrate a good understanding of both the physics and the chemistry behind the system and points to a general route for designing new families of self-propelled particles.}, author = {Palacci, Jérémie A and Sacanna, S. and Kim, S.-H. and Yi, G.-R. and Pine, D. J. and Chaikin, P. M.}, issn = {1471-2962}, journal = {Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences}, keywords = {General Engineering, General Physics and Astronomy, General Mathematics}, number = {2029}, publisher = {The Royal Society}, title = {{Light-activated self-propelled colloids}}, doi = {10.1098/rsta.2013.0372}, volume = {372}, year = {2014}, } @article{10384, abstract = {Recent studies aimed at investigating artificial analogs of bacterial colonies have shown that low-density suspensions of self-propelled particles confined in two dimensions can assemble into finite aggregates that merge and split, but have a typical size that remains constant (living clusters). In this Letter, we address the problem of the formation of living clusters and crystals of active particles in three dimensions. We study two systems: self-propelled particles interacting via a generic attractive potential and colloids that can move toward each other as a result of active agents (e.g., by molecular motors). In both cases, fluidlike “living” clusters form. We explain this general feature in terms of the balance between active forces and regression to thermodynamic equilibrium. This balance can be quantified in terms of a dimensionless number that allows us to collapse the observed clustering behavior onto a universal curve. We also discuss how active motion affects the kinetics of crystal formation.}, author = {Mognetti, B. M. and Šarić, Anđela and Angioletti-Uberti, S. and Cacciuto, A. and Valeriani, C. and Frenkel, D.}, issn = {1079-7114}, journal = {Physical Review Letters}, keywords = {general physics and astronomy}, number = {24}, publisher = {American Physical Society}, title = {{Living clusters and crystals from low-density suspensions of active colloids}}, doi = {10.1103/physrevlett.111.245702}, volume = {111}, year = {2013}, } @article{10385, abstract = {We show how self-assembly of sticky nanoparticles can drive radial collapse of thin-walled nanotubes. Using numerical simulations, we study the transition as a function of the geometric and elastic parameters of the nanotube and the binding strength of the nanoparticles. We find that it is possible to derive a simple scaling law relating all these parameters, and estimate bounds for the onset conditions leading to the collapse of the nanotube. We also study the reverse process – the nanoparticle release from the folded state – and find that the stability of the collapsed state can be greatly improved by increasing the bending rigidity of the nanotubes. Our results suggest ways to strengthen the mechanical properties of nanotubes, but also indicate that the control of nanoparticle self-assembly on these nanotubes can lead to nanoparticle-laden responsive materials.}, author = {Napoli, Joseph A. and Šarić, Anđela and Cacciuto, Angelo}, issn = {1744-6848}, journal = {Soft Matter}, keywords = {condensed matter physics, general chemistry}, number = {37}, pages = {8881--8886}, publisher = {Royal Society of Chemistry}, title = {{Collapsing nanoparticle-laden nanotubes}}, doi = {10.1039/c3sm51495a}, volume = {9}, year = {2013}, } @article{10386, abstract = {In this paper we review recent numerical and theoretical developments of particle self-assembly on fluid and elastic membranes and compare them to available experimental realizations. We discuss the problem and its applications in biology and materials science, and give an overview of numerical models and strategies to study these systems across all length-scales. As this is a very broad field, this review focuses exclusively on surface-driven aggregation of nanoparticles that are at least one order of magnitude larger than the surface thickness and are adsorbed onto it. In this regime, all chemical details of the surface can be ignored in favor of a coarse-grained representation, and the collective behavior of many particles can be monitored and analyzed. We review the existing literature on how the mechanical properties and the geometry of the surface affect the structure of the particle aggregates and how these can drive shape deformation on the surface.}, author = {Šarić, Anđela and Cacciuto, Angelo}, issn = {1744-6848}, journal = {Soft Matter}, keywords = {condensed matter physics, general chemistry}, number = {29}, publisher = {Royal Society of Chemistry}, title = {{Self-assembly of nanoparticles adsorbed on fluid and elastic membranes}}, doi = {10.1039/c3sm50188d}, volume = {9}, year = {2013}, } @article{8502, abstract = {The famous ergodic hypothesis suggests that for a typical Hamiltonian on a typical energy surface nearly all trajectories are dense. KAM theory disproves it. Ehrenfest (The Conceptual Foundations of the Statistical Approach in Mechanics. Ithaca, NY: Cornell University Press, 1959) and Birkhoff (Collected Math Papers. Vol 2, New York: Dover, pp 462–465, 1968) stated the quasi-ergodic hypothesis claiming that a typical Hamiltonian on a typical energy surface has a dense orbit. This question is wide open. Herman (Proceedings of the International Congress of Mathematicians, Vol II (Berlin, 1998). Doc Math 1998, Extra Vol II, Berlin: Int Math Union, pp 797–808, 1998) proposed to look for an example of a Hamiltonian near H0(I)=⟨I,I⟩2 with a dense orbit on the unit energy surface. In this paper we construct a Hamiltonian H0(I)+εH1(θ,I,ε) which has an orbit dense in a set of maximal Hausdorff dimension equal to 5 on the unit energy surface.}, author = {Kaloshin, Vadim and Saprykina, Maria}, issn = {0010-3616}, journal = {Communications in Mathematical Physics}, keywords = {Mathematical Physics, Statistical and Nonlinear Physics}, number = {3}, pages = {643--697}, publisher = {Springer Nature}, title = {{An example of a nearly integrable Hamiltonian system with a trajectory dense in a set of maximal Hausdorff dimension}}, doi = {10.1007/s00220-012-1532-x}, volume = {315}, year = {2012}, } @article{10387, abstract = {We report numerical simulations of membrane tubulation driven by large colloidal particles. Using Monte Carlo simulations we study how the process depends on particle size and binding strength, and present accurate free energy calculations to sort out how tube formation compares with the competing budding process. We find that tube formation is a result of the collective behavior of the particles adhering on the surface, and it occurs for binding strengths that are smaller than those required for budding. We also find that long linear aggregates of particles forming on the membrane surface act as nucleation seeds for tubulation by lowering the free energy barrier associated to the process.}, author = {Šarić, Anđela and Cacciuto, Angelo}, issn = {1079-7114}, journal = {Physical Review Letters}, keywords = {general physics and astronomy}, number = {18}, publisher = {American Physical Society}, title = {{Mechanism of membrane tube formation induced by adhesive nanocomponents}}, doi = {10.1103/physrevlett.109.188101}, volume = {109}, year = {2012}, } @article{10388, abstract = {Using computer simulations, we show that lipid membranes can mediate linear aggregation of spherical nanoparticles binding to it for a wide range of biologically relevant bending rigidities. This result is in net contrast with the isotropic aggregation of nanoparticles on fluid interfaces or the expected clustering of isotropic insertions in biological membranes. We present a phase diagram indicating where linear aggregation is expected and compute explicitly the free-energy barriers associated with linear and isotropic aggregation. Finally, we provide simple scaling arguments to explain this phenomenology.}, author = {Šarić, Anđela and Cacciuto, Angelo}, issn = {1079-7114}, journal = {Physical Review Letters}, keywords = {general physics and astronomy}, number = {11}, publisher = {American Physical Society}, title = {{Fluid membranes can drive linear aggregation of adsorbed spherical nanoparticles}}, doi = {10.1103/physrevlett.108.118101}, volume = {108}, year = {2012}, } @article{8469, abstract = {The accurate experimental determination of dipolar-coupling constants for one-bond heteronuclear dipolar couplings in solids is a key for the quantification of the amplitudes of motional processes. Averaging of the dipolar coupling reports on motions on time scales up to the inverse of the coupling constant, in our case tens of microseconds. Combining dipolar-coupling derived order parameters that characterize the amplitudes of the motion with relaxation data leads to a more precise characterization of the dynamical parameters and helps to disentangle the amplitudes and the time scales of the motional processes, which impact relaxation rates in a highly correlated way. Here. we describe and characterize an improved experimental protocol – based on REDOR – to measure these couplings in perdeuterated proteins with a reduced sensitivity to experimental missettings. Because such effects are presently the dominant source of systematic errors in experimental dipolar-coupling measurements, these compensated experiments should help to significantly improve the precision of such data. A detailed comparison with other commonly used pulse sequences (T-MREV, phase-inverted CP,R18 5/2, and R18 7/1) is provided.}, author = {Schanda, Paul and Meier, Beat H. and Ernst, Matthias}, issn = {1090-7807}, journal = {Journal of Magnetic Resonance}, keywords = {Nuclear and High Energy Physics, Biophysics, Biochemistry, Condensed Matter Physics}, number = {2}, pages = {246--259}, publisher = {Elsevier}, title = {{Accurate measurement of one-bond H–X heteronuclear dipolar couplings in MAS solid-state NMR}}, doi = {10.1016/j.jmr.2011.03.015}, volume = {210}, year = {2011}, } @article{8470, abstract = {Adding a new dimension: 4D or 3D proton‐detected spectra of perdeuterated protein samples with 1H labelled amides and methyl groups permit collecting unambiguous distance restraints with high sensitivity and determining protein structure by solid‐state NMR (see picture).}, author = {Huber, Matthias and Hiller, Sebastian and Schanda, Paul and Ernst, Matthias and Böckmann, Anja and Verel, René and Meier, Beat H.}, issn = {1439-4235}, journal = {ChemPhysChem}, keywords = {Physical and Theoretical Chemistry, Atomic and Molecular Physics, and Optics}, number = {5}, pages = {915--918}, publisher = {Wiley}, title = {{A proton-detected 4D solid-state NMR experiment for protein structure determination}}, doi = {10.1002/cphc.201100062}, volume = {12}, year = {2011}, } @article{10389, abstract = {We perform numerical simulations to study self-assembly of nanoparticles mediated by an elastic planar surface. We show how the nontrivial elastic response to deformations of these surfaces leads to anisotropic interactions between the particles resulting in aggregates having different geometrical features. The morphology of the patterns can be controlled by the mechanical properties of the surface and the strength of the particle adhesion. We use simple scaling arguments to understand the formation of the different structures, and we show how the adhering particles can cause the underlying elastic substrate to wrinkle if two of its opposite edges are clamped. Finally, we discuss the implications of our results and suggest how elastic surfaces could be used in nanofabrication.}, author = {Šarić, Anđela and Cacciuto, Angelo}, issn = {1744-6848}, journal = {Soft Matter}, keywords = {condensed matter physics, general chemistry}, number = {18}, publisher = {Royal Society of Chemistry}, title = {{Soft elastic surfaces as a platform for particle self-assembly}}, doi = {10.1039/c1sm05773a}, volume = {7}, year = {2011}, } @article{10127, abstract = {We use numerical simulations to show how noninteracting hard particles binding to a deformable elastic shell may self-assemble into a variety of linear patterns. This is a result of the nontrivial elastic response to deformations of shells. The morphology of the patterns can be controlled by the mechanical properties of the surface, and can be fine-tuned by varying the binding energy of the particles. We also repeat our calculations for a fully flexible chain and find that the chain conformations follow patterns similar to those formed by the nanoparticles under analogous conditions. We propose a simple way of understanding and sorting the different structures and relate it to the underlying shape transition of the shell. Finally, we discuss the implications of our results.}, author = {Šarić, Anđela and Cacciuto, Angelo}, issn = {1744-683X}, journal = {Soft Matter}, keywords = {condensed matter physics, general chemistry}, number = {5}, pages = {1874--1878}, publisher = {Royal Society of Chemistry (RSC)}, title = {{Particle self-assembly on soft elastic shells}}, doi = {10.1039/c0sm01143f}, volume = {7}, year = {2010}, } @article{10128, abstract = {An extensive computational study of the conformational preferences of three capped dipeptides: Ac-Xxx-Phe-NH2, Xxx = Gly, Ala, Val is reported. On the basis of local second-order Møller–Plesset perturbation theory (LMP2) and DFT computations we were able to identify the experimentally observed conformers as γL–γL(g−) and β-turn I(g+) in Ac-Gly-Phe-NH2, and Ac-Ala-Phe-NH2, and as the closely related γL(g+)–γL(g−) and β-turn I(a,g+) in Ac-Val-Phe-NH2. In contrast to the experimental observation that peptides with bulky side chain have a propensity for β-turns, we show that in Ac-Val-Phe-NH2 the minimum energy structure corresponds to the experimentally non detected β-strand.}, author = {Šarić, Anđela and Hrenar, T. and Mališ, M. and Došlić, N.}, issn = {1463-9076}, journal = {Physical Chemistry Chemical Physics}, keywords = {Physical and Theoretical Chemistry, General Physics and Astronomy}, number = {18}, pages = {4678--4685}, publisher = {Royal Society of Chemistry }, title = {{Quantum mechanical study of secondary structure formation in protected dipeptides}}, doi = {10.1039/b923041f}, volume = {12}, year = {2010}, } @article{10391, abstract = {We use numerical simulations to show how a fully flexible filament binding to a deformable cylindrical surface may acquire a macroscopic persistence length and a helical conformation. This is a result of the nontrivial elastic response to deformations of elastic sheets. We find that the filament’s helical pitch is completely determined by the mechanical properties of the surface, and can be easily tuned by varying the surface stretching rigidity. We propose simple scaling arguments to understand the physical mechanism behind this phenomenon and present a phase diagram indicating under what conditions one should expect a fully flexible chain to behave as a helical semiflexible filament. Finally, we discuss the implications of our results.}, author = {Šarić, Anđela and Pàmies, Josep C. and Cacciuto, Angelo}, issn = {1079-7114}, journal = {Physical Review Letters}, keywords = {general physics and astronomy}, number = {22}, publisher = {American Physical Society}, title = {{Effective elasticity of a flexible filament bound to a deformable cylindrical surface}}, doi = {10.1103/physrevlett.104.226101}, volume = {104}, year = {2010}, } @article{13416, abstract = {The reversible molecular template-directed self-assembly of gold nanoparticles (AuNPs), a process which relies solely on noncovalent bonding interactions, has been demonstrated by high-resolution transmission electron microscopy (HR-TEM). By employing a well-known host−guest binding motif, the AuNPs have been systemized into discrete dimers, trimers, and tetramers. These nanoparticulate twins, triplets, and quadruplets, which can be disassembled and reassembled either chemically or electrochemically, can be coalesced into larger, permanent polygonal structures by thermal treatment using a focused HR-TEM electron beam.}, author = {Olson, Mark A. and Coskun, Ali and Klajn, Rafal and Fang, Lei and Dey, Sanjeev K. and Browne, Kevin P. and Grzybowski, Bartosz A. and Stoddart, J. Fraser}, issn = {1530-6992}, journal = {Nano Letters}, keywords = {Mechanical Engineering, Condensed Matter Physics, General Materials Science, General Chemistry, Bioengineering}, number = {9}, pages = {3185--3190}, publisher = {American Chemical Society}, title = {{Assembly of polygonal nanoparticle clusters directed by reversible noncovalent bonding interactions}}, doi = {10.1021/nl901385c}, volume = {9}, year = {2009}, } @article{8482, abstract = {The SOFAST-HMQC experiment [P. Schanda, B. Brutscher, Very fast two-dimensional NMR spectroscopy for real-time investigation of dynamic events in proteins on the time scale of seconds, J. Am. Chem. Soc. 127 (2005) 8014–8015] allows recording two-dimensional correlation spectra of macromolecules such as proteins in only a few seconds acquisition time. To achieve the highest possible sensitivity, SOFAST-HMQC experiments are preferably performed on high-field NMR spectrometers equipped with cryogenically cooled probes. The duty cycle of over 80% in fast-pulsing SOFAST-HMQC experiments, however, may cause problems when using a cryogenic probe. Here we introduce SE-IPAP-SOFAST-HMQC, a new pulse sequence that provides comparable sensitivity to standard SOFAST-HMQC, while avoiding heteronuclear decoupling during 1H detection, and thus significantly reducing the radiofrequency load of the probe during the experiment. The experiment is also attractive for fast and sensitive measurement of heteronuclear one-bond spin coupling constants.}, author = {Kern, Thomas and Schanda, Paul and Brutscher, Bernhard}, issn = {1090-7807}, journal = {Journal of Magnetic Resonance}, keywords = {Nuclear and High Energy Physics, Biophysics, Biochemistry, Condensed Matter Physics}, number = {2}, pages = {333--338}, publisher = {Elsevier}, title = {{Sensitivity-enhanced IPAP-SOFAST-HMQC for fast-pulsing 2D NMR with reduced radiofrequency load}}, doi = {10.1016/j.jmr.2007.11.015}, volume = {190}, year = {2008}, } @article{13423, abstract = {Supraspheres (SS) composed of hundreds to thousands of metal nanoparticles (NPs) and crosslinked by dithiol linkers are assembled into larger structures, which are subsequently converted into nanoporous metals (NMs). Conversion is achieved by heating which removes organic molecules stabilizing the NPs and allows for NP fusion. Heating of SS solutions leads to NMs of overall macroscopic dimensions; localized radiation using collimated electron beam is used to prepare metallized surface micropatterns. Depending on the composition of supraspherical precursors, nanoporous materials composed of up to three metals can be obtained. Strategies for controlling pore size and nanoscale surface roughness of these materials are discussed.}, author = {Klajn, Rafal and Gray, Timothy P. and Wesson, Paul J. and Myers, Benjamin D. and Dravid, Vinayak P. and Smoukov, Stoyan K. and Grzybowski, Bartosz A.}, issn = {1616-3028}, journal = {Advanced Functional Materials}, keywords = {Electrochemistry, Condensed Matter Physics, Biomaterials, Electronic, Optical and Magnetic Materials}, number = {18}, pages = {2763--2769}, publisher = {Wiley}, title = {{Bulk synthesis and surface patterning of nanoporous metals and alloys from supraspherical nanoparticle aggregates}}, doi = {10.1002/adfm.200800293}, volume = {18}, year = {2008}, } @article{13426, abstract = {Photoswelling of thin films of dichromated gelatin provides a basis for fabrication of multilevel surface reliefs via sequential UV illumination through different photomasks. The remarkable feature of this simple, benchtop technique is that by adjusting irradiation times, film thickness, or its hydration state the heights of the developed features can be varied from few nanometers to tens of microns. After UV exposure, the surface structures can be replicated faithfully into either soft or hard PDMS stamps.}, author = {Paszewski, Maciej and Smoukov, Stoyan K. and Klajn, Rafal and Grzybowski, Bartosz A.}, issn = {1520-5827}, journal = {Langmuir}, keywords = {Electrochemistry, Spectroscopy, Surfaces and Interfaces, Condensed Matter Physics, General Materials Science}, number = {10}, pages = {5419--5422}, publisher = {American Chemical Society}, title = {{Multilevel surface nano- and microstructuring via sequential photoswelling of dichromated gelatin}}, doi = {10.1021/la062982c}, volume = {23}, year = {2007}, } @article{9149, abstract = {The interaction of tidal currents with sea-floor topography results in the radiation of internal gravity waves into the ocean interior. These waves are called internal tides and their dissipation due to nonlinear wave breaking and concomitant three-dimensional turbulence could play an important role in the mixing of the abyssal ocean, and hence in controlling the large-scale ocean circulation. As part of on-going work aimed at providing a theory for the vertical distribution of wave breaking over sea-floor topography, in this paper we investigate the instability of internal tides in a very simple linear model that helps us to relate the formation of unstable regions to simple features in the sea-floor topography. For two-dimensional tides over one-dimensional topography we find that the formation of overturning instabilities is closely linked to the singularities in the topography shape and that it is possible to have stable waves at the sea floor and unstable waves in the ocean interior above. For three-dimensional tides over two-dimensional topography there is in addition an effect of geometric focusing of wave energy into localized regions of high wave amplitude, and we investigate this focusing effect in simple examples. Overall, we find that the distribution of unstable wave breaking regions can be highly non-uniform even for very simple idealized topography shapes.}, author = {Bühler, Oliver and Muller, Caroline J}, issn = {0022-1120}, journal = {Journal of Fluid Mechanics}, keywords = {mechanical engineering, mechanics of materials, condensed matter physics}, pages = {1--28}, publisher = {Cambridge University Press}, title = {{Instability and focusing of internal tides in the deep ocean}}, doi = {10.1017/s0022112007007410}, volume = {588}, year = {2007}, } @article{8490, abstract = {We demonstrate the feasibility of recording 1H–15N correlation spectra of proteins in only one second of acquisition time. The experiment combines recently proposed SOFAST-HMQC with Hadamard-type 15N frequency encoding. This allows site-resolved real-time NMR studies of kinetic processes in proteins with an increased time resolution. The sensitivity of the experiment is sufficient to be applicable to a wide range of molecular systems available at millimolar concentration on a high magnetic field spectrometer.}, author = {Schanda, Paul and Brutscher, Bernhard}, issn = {1090-7807}, journal = {Journal of Magnetic Resonance}, keywords = {Nuclear and High Energy Physics, Biophysics, Biochemistry, Condensed Matter Physics}, number = {2}, pages = {334--339}, publisher = {Elsevier}, title = {{Hadamard frequency-encoded SOFAST-HMQC for ultrafast two-dimensional protein NMR}}, doi = {10.1016/j.jmr.2005.10.007}, volume = {178}, year = {2006}, }