1
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He H, Liang H, Chu M, Jiang Z, de Pablo JJ, Tirrell MV, Narayanan S, Chen W. Transport coefficient approach for characterizing nonequilibrium dynamics in soft matter. Proc Natl Acad Sci U S A 2024; 121:e2401162121. [PMID: 39042671 PMCID: PMC11295068 DOI: 10.1073/pnas.2401162121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 06/16/2024] [Indexed: 07/25/2024] Open
Abstract
Nonequilibrium states in soft condensed matter require a systematic approach to characterize and model materials, enhancing predictability and applications. Among the tools, X-ray photon correlation spectroscopy (XPCS) provides exceptional temporal and spatial resolution to extract dynamic insight into the properties of the material. However, existing models might overlook intricate details. We introduce an approach for extracting the transport coefficient, denoted as [Formula: see text], from the XPCS studies. This coefficient is a fundamental parameter in nonequilibrium statistical mechanics and is crucial for characterizing transport processes within a system. Our method unifies the Green-Kubo formulas associated with various transport coefficients, including gradient flows, particle-particle interactions, friction matrices, and continuous noise. We achieve this by integrating the collective influence of random and systematic forces acting on the particles within the framework of a Markov chain. We initially validated this method using molecular dynamics simulations of a system subjected to changes in temperatures over time. Subsequently, we conducted further verification using experimental systems reported in the literature and known for their complex nonequilibrium characteristics. The results, including the derived [Formula: see text] and other relevant physical parameters, align with the previous observations and reveal detailed dynamical information in nonequilibrium states. This approach represents an advancement in XPCS analysis, addressing the growing demand to extract intricate nonequilibrium dynamics. Further, the methods presented are agnostic to the nature of the material system and can be potentially expanded to hard condensed matter systems.
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Affiliation(s)
- HongRui He
- Materials Science Division and Center for Molecular Engineering, Argonne National Laboratory, Lemont, IL60439
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL60637
| | - Heyi Liang
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL60637
| | - Miaoqi Chu
- X-Ray Science Division, Advanced Photon Source, Argonne National Laboratory, Lemont, IL60439
| | - Zhang Jiang
- X-Ray Science Division, Advanced Photon Source, Argonne National Laboratory, Lemont, IL60439
| | - Juan J. de Pablo
- Materials Science Division and Center for Molecular Engineering, Argonne National Laboratory, Lemont, IL60439
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL60637
| | - Matthew V. Tirrell
- Materials Science Division and Center for Molecular Engineering, Argonne National Laboratory, Lemont, IL60439
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL60637
| | - Suresh Narayanan
- X-Ray Science Division, Advanced Photon Source, Argonne National Laboratory, Lemont, IL60439
| | - Wei Chen
- Materials Science Division and Center for Molecular Engineering, Argonne National Laboratory, Lemont, IL60439
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL60637
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2
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Gasser U, Zhou B. Accurate detection of spherical objects in a complex background. OPTICS EXPRESS 2021; 29:37048-37065. [PMID: 34808784 DOI: 10.1364/oe.434652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 10/02/2021] [Indexed: 06/13/2023]
Abstract
The automated detection of particles in microscopy images has become a routinely used method for quantitative image analysis in biology, physics, and other research fields. While the majority of particle detection algorithms have been developed for bulk materials, the detection of particles in a heterogenous environment due to surfaces or other objects in the studied material is of great interest. However, particle detection is hindered by a complex background due to the diffraction of light resulting in a decreased contrast and image noise. We present a new heuristic method for the reliable detection of spherical particles that suppresses false detections due to a heterogenous background without additional background measurements. Further, we discuss methods to obtain particle coordinates with improved accuracy and compare with other methods, in particular with that of Crocker and Grier.
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3
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Chardac A, Shankar S, Marchetti MC, Bartolo D. Emergence of dynamic vortex glasses in disordered polar active fluids. Proc Natl Acad Sci U S A 2021; 118:e2018218118. [PMID: 33658364 PMCID: PMC7958234 DOI: 10.1073/pnas.2018218118] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
In equilibrium, disorder conspires with topological defects to redefine the ordered states of matter in systems as diverse as crystals, superconductors, and liquid crystals. Far from equilibrium, however, the consequences of quenched disorder on active condensed matter remain virtually uncharted. Here, we reveal a state of strongly disordered active matter with no counterparts in equilibrium: a dynamical vortex glass. Combining microfluidic experiments and theory, we show how colloidal flocks collectively cruise through disordered environments without relaxing the topological singularities of their flows. The resulting state is highly dynamical but the flow patterns, shaped by a finite density of frozen vortices, are stationary and exponentially degenerated. Quenched isotropic disorder acts as a random gauge field turning active liquids into dynamical vortex glasses. We argue that this robust mechanism should shape the collective dynamics of a broad class of disordered active matter, from synthetic active nematics to collections of living cells exploring heterogeneous media.
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Affiliation(s)
- Amélie Chardac
- Université de Lyon, École Normale Supérieure de Lyon, Université Claude Bernard, CNRS, Laboratoire de Physique, F-69342 Lyon, France
| | - Suraj Shankar
- Department of Physics, Harvard University, Cambridge, MA 02138
| | | | - Denis Bartolo
- Université de Lyon, École Normale Supérieure de Lyon, Université Claude Bernard, CNRS, Laboratoire de Physique, F-69342 Lyon, France;
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4
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Liber SR, Indech G, van der Wee EB, Butenko AV, Kodger TE, Lu PJ, Schofield AB, Weitz DA, van Blaaderen A, Sloutskin E. Axial Confocal Tomography of Capillary-Contained Colloidal Structures. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:13343-13349. [PMID: 29043816 DOI: 10.1021/acs.langmuir.7b03039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Confocal microscopy is widely used for three-dimensional (3D) sample reconstructions. Arguably, the most significant challenge in such reconstructions is posed by the resolution along the optical axis being significantly lower than in the lateral directions. In addition, the imaging rate is lower along the optical axis in most confocal architectures, prohibiting reliable 3D reconstruction of dynamic samples. Here, we demonstrate a very simple, cheap, and generic method of multiangle microscopy, allowing high-resolution high-rate confocal slice collection to be carried out with capillary-contained colloidal samples in a wide range of slice orientations. This method, realizable with any common confocal architecture and recently implemented with macroscopic specimens enclosed in rotatable cylindrical capillaries, allows 3D reconstructions of colloidal structures to be verified by direct experiments and provides a solid testing ground for complex reconstruction algorithms. In this paper, we focus on the implementation of this method for dense nonrotatable colloidal samples, contained in complex-shaped capillaries. Additionally, we discuss strategies to minimize potential pitfalls of this method, such as the artificial appearance of chain-like particle structures.
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Affiliation(s)
- Shir R Liber
- Physics Department and Bar-Ilan Institute of Nanotechnology & Advanced Materials, Bar-Ilan University , Ramat-Gan 5290002, Israel
| | - Ganit Indech
- Physics Department and Bar-Ilan Institute of Nanotechnology & Advanced Materials, Bar-Ilan University , Ramat-Gan 5290002, Israel
| | - Ernest B van der Wee
- Soft Condensed Matter, Debye Institute for NanoMaterials Science, Utrecht University , Princetonplein 1, 3584 CC Utrecht, The Netherlands
| | - Alexander V Butenko
- Physics Department and Bar-Ilan Institute of Nanotechnology & Advanced Materials, Bar-Ilan University , Ramat-Gan 5290002, Israel
| | - Thomas E Kodger
- Physical Chemistry and Soft Matter, Wageningen University & Research , Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Peter J Lu
- Department of Physics and SEAS, Harvard University , Cambridge, Massachusetts 02138, United States
| | - Andrew B Schofield
- The School of Physics and Astronomy, University of Edinburgh , Edinburgh EH9 3FD, U.K
| | - David A Weitz
- Department of Physics and SEAS, Harvard University , Cambridge, Massachusetts 02138, United States
| | - Alfons van Blaaderen
- Soft Condensed Matter, Debye Institute for NanoMaterials Science, Utrecht University , Princetonplein 1, 3584 CC Utrecht, The Netherlands
| | - Eli Sloutskin
- Physics Department and Bar-Ilan Institute of Nanotechnology & Advanced Materials, Bar-Ilan University , Ramat-Gan 5290002, Israel
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5
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Kodger TE, Lu PJ, Wiseman GR, Weitz DA. Stable, Fluorescent Polymethylmethacrylate Particles for the Long-Term Observation of Slow Colloidal Dynamics. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:6382-6389. [PMID: 28560881 DOI: 10.1021/acs.langmuir.7b00852] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Suspensions of solid micron-scale colloidal particles in liquid solvents are a foundational model system used to explore a wide range of phase transitions, including crystallization, gelation, spinodal decomposition, and the glass transition. One of the most commonly used systems for these investigations is the fluorescent spherical particles of polymethylmethacrylate (PMMA) suspended in a mixture of nonpolar solvents that match the density and the refractive index of the particles to minimize sedimentation and scattering. However, the particles can swell in these solvents, changing their size and density, and may leak the fluorescent dye over days to weeks; this constrains the exploration of slow and kinetically limited processes, such as near-boundary phase separation or the glass transition. In this paper, we produce PMMA colloidal particles that employ polymerizable and photostable cyanine-based fluorescent monomers spanning the range of visible wavelengths and a polymeric stabilizer prepared from polydimethylsiloxane, PDMS-graft-PMMA. Using microcalorimetry, we characterize the thermodynamics of an accelerated equilibration process for these dispersions in the buoyancy- and refractive-index-matching solvents. We use confocal differential dynamic microscopy to demonstrate that they behave as hard spheres. The suspended particles are stable for months to years, maintaining fixed particle size and density, and do not leak dye. Thus, these particles enable longer term experiments than may have been possible earlier; we demonstrate this by observing spinodal decomposition in a mixture of these particles with a depletant polymer in the microgravity environment of the International Space Station. Using fluorescence microscopy, we observe coarsening over several months and measure the growth of the characteristic length scale to be a fraction of a picometer per second; this rate is among the slowest observed in a phase-separating system. Our protocols should facilitate the synthesis of a variety of particles.
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Affiliation(s)
- Thomas E Kodger
- Department of Physics and SEAS, Harvard University , Cambridge, Massachusetts 02138, United States
| | - Peter J Lu
- Department of Physics and SEAS, Harvard University , Cambridge, Massachusetts 02138, United States
| | - G Reid Wiseman
- International Space Station, Low Earth Orbit, and NASA Johnson Space Center , Houston, Texas 77058, United States
| | - David A Weitz
- Department of Physics and SEAS, Harvard University , Cambridge, Massachusetts 02138, United States
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6
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Zhao W, Sheng Z, Qiu L, Wang Y, Shao R. Bilateral fitting subtracting confocal microscopy. APPLIED OPTICS 2016; 55:10269-10275. [PMID: 28059245 DOI: 10.1364/ao.55.010269] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
This paper proposes a bilateral fitting subtracting confocal microscopy (BFSCM) based on the optical arrangement of conventional confocal microscopy (CM). BFSCM first uses the data in both sides of a confocal axial response curve, which are very sensitive to the axial position of the sample, for respective linear fitting to obtain two fitting straight lines, and then obtains a difference confocal line by subtraction of the two fitting lines. Finally, it calculates the zero position of the difference confocal line to precisely capture the focus position of the confocal system, and thereby achieving a high-precision measurement of the 3D structure of the sample. The theoretical analyses and experiments indicate that BFSCM can improve the axial resolution, and has anti-interference capability and focusing ability with bipolar absolute zero point tracking, while it does not change the structure and lateral resolution of CM. BFSCM provides a novel method for the improvement of CM axial resolution.
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7
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Photo-Crosslinkable Colloids: From Fluid Structure and Dynamics of Spheres to Suspensions of Ellipsoids. Gels 2016; 2:gels2040029. [PMID: 30674159 PMCID: PMC6318651 DOI: 10.3390/gels2040029] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 11/03/2016] [Accepted: 11/07/2016] [Indexed: 11/16/2022] Open
Abstract
Recently-developed photo-crosslinkable PMMA (polymethylmethacrylate) colloidal spheres are a highly promising system for fundamental studies in colloidal physics and may have a wide range of future technological applications. We synthesize these colloids and characterize their size distribution. Their swelling in a density- and index- matching organic solvent system is demonstrated and we employ dynamic light scattering (DLS), as also the recently-developed confocal differential dynamic microscopy (ConDDM), to characterize the structure and the dynamics of a fluid bulk suspension of such colloids at different particle densities, detecting significant particle charging effects. We stretch these photo-crosslinkable spheres into ellipsoids. The fact that the ellipsoids are cross-linked allows them to be fluorescently stained, permitting a dense suspension of ellipsoids, a simple model of fluid matter, to be imaged by direct confocal microscopy.
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8
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Jensen KE, Nakamura N. Note: An iterative algorithm to improve colloidal particle locating. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2016; 87:066103. [PMID: 27370504 DOI: 10.1063/1.4952992] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Confocal microscopy of colloids combined with digital image processing has become a powerful tool in soft matter physics and materials science. Together, these techniques enable locating and tracking of more than half a million individual colloidal particles at once. However, despite improvements in locating algorithms that improve position accuracy, it remains challenging to locate all particles in a densely packed, three dimensional colloid without erroneously identifying the same particle more than once. We present a simple iterative algorithm that mitigates both the "missed particle" and "double counting" problems while simultaneously reducing sensitivity to the specific choice of input parameters. It is also useful for analyzing images with spatially varying brightness in which a single set of input parameters is not appropriate for all particles. The algorithm is easy to implement and compatible with existing particle locating software.
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Affiliation(s)
- K E Jensen
- Department of Physics, Harvard University, Cambridge, Massachusetts 02138, USA
| | - N Nakamura
- Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
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9
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Cohen AP, Dorosz S, Schofield AB, Schilling T, Sloutskin E. Structural Transition in a Fluid of Spheroids: A Low-Density Vestige of Jamming. PHYSICAL REVIEW LETTERS 2016; 116:098001. [PMID: 26991202 DOI: 10.1103/physrevlett.116.098001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Indexed: 06/05/2023]
Abstract
A thermodynamically equilibrated fluid of hard spheroids is a simple model of liquid matter. In this model, the coupling between the rotational degrees of freedom of the constituent particles and their translations may be switched off by a continuous deformation of a spheroid of aspect ratio t into a sphere (t=1). We demonstrate, by experiments, theory, and computer simulations, that dramatic nonanalytic changes in structure and thermodynamics of the fluids take place, as the coupling between rotations and translations is made to vanish. This nonanalyticity, reminiscent of a second-order liquid-liquid phase transition, is not a trivial consequence of the shape of an individual particle. Rather, free volume considerations relate the observed transition to a similar nonanalyticity at t=1 in structural properties of jammed granular ellipsoids. This observation suggests a deep connection to exist between the physics of jamming and the thermodynamics of simple fluids.
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Affiliation(s)
- A P Cohen
- Physics Department and Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - S Dorosz
- Research Unit for Physics and Materials Science, Université du Luxembourg, L-1511 Luxembourg, Luxembourg
| | - A B Schofield
- School of Physics and Astronomy, University of Edinburgh, Edinburgh EH9 3FD, United Kingdom
| | - T Schilling
- Research Unit for Physics and Materials Science, Université du Luxembourg, L-1511 Luxembourg, Luxembourg
| | - E Sloutskin
- Physics Department and Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan 5290002, Israel
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10
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Besseling TH, Hermes M, Kuijk A, de Nijs B, Deng TS, Dijkstra M, Imhof A, van Blaaderen A. Determination of the positions and orientations of concentrated rod-like colloids from 3D microscopy data. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2015; 27:194109. [PMID: 25922931 DOI: 10.1088/0953-8984/27/19/194109] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Confocal microscopy in combination with real-space particle tracking has proven to be a powerful tool in scientific fields such as soft matter physics, materials science and cell biology. However, 3D tracking of anisotropic particles in concentrated phases remains not as optimized compared to algorithms for spherical particles. To address this problem, we developed a new particle-fitting algorithm that can extract the positions and orientations of fluorescent rod-like particles from three dimensional confocal microscopy data stacks. The algorithm is tailored to work even when the fluorescent signals of the particles overlap considerably and a threshold method and subsequent clusters analysis alone do not suffice. We demonstrate that our algorithm correctly identifies all five coordinates of uniaxial particles in both a concentrated disordered phase and a liquid-crystalline smectic-B phase. Apart from confocal microscopy images, we also demonstrate that the algorithm can be used to identify nanorods in 3D electron tomography reconstructions. Lastly, we determined the accuracy of the algorithm using both simulated and experimental confocal microscopy data-stacks of diffusing silica rods in a dilute suspension. This novel particle-fitting algorithm allows for the study of structure and dynamics in both dilute and dense liquid-crystalline phases (such as nematic, smectic and crystalline phases) as well as the study of the glass transition of rod-like particles in three dimensions on the single particle level.
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11
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Kanai T, Boon N, Lu PJ, Sloutskin E, Schofield AB, Smallenburg F, van Roij R, Dijkstra M, Weitz DA. Crystallization and reentrant melting of charged colloids in nonpolar solvents. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015; 91:030301. [PMID: 25871032 DOI: 10.1103/physreve.91.030301] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Indexed: 06/04/2023]
Abstract
We explore the crystallization of charged colloidal particles in a nonpolar solvent mixture. We simultaneously charge the particles and add counterions to the solution with aerosol-OT (AOT) reverse micelles. At low AOT concentrations, the charged particles crystallize into body-centered-cubic (bcc) or face-centered-cubic (fcc) Wigner crystals; at high AOT concentrations, the increased screening drives a thus far unobserved reentrant melting transition. We observe an unexpected scaling of the data with particle size, and account for all behavior with a model that quantitatively predicts both the reentrant melting and the data collapse.
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Affiliation(s)
- Toshimitsu Kanai
- Department of Physics and SEAS, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Niels Boon
- Institute for Theoretical Physics, Utrecht University, Leuvenlaan 4, 3584 CE Utrecht, The Netherlands
| | - Peter J Lu
- Department of Physics and SEAS, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Eli Sloutskin
- Department of Physics and SEAS, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Andrew B Schofield
- The School of Physics, University of Edinburgh, Edinburgh EH9 3FD, United Kingdom
| | - Frank Smallenburg
- Soft Condensed Matter, Debye Institute for Nanomaterials Science, Utrecht University, Princetonplein 5, 3584 CC Utrecht, The Netherlands
| | - René van Roij
- Institute for Theoretical Physics, Utrecht University, Leuvenlaan 4, 3584 CE Utrecht, The Netherlands
| | - Marjolein Dijkstra
- Soft Condensed Matter, Debye Institute for Nanomaterials Science, Utrecht University, Princetonplein 5, 3584 CC Utrecht, The Netherlands
| | - David A Weitz
- Department of Physics and SEAS, Harvard University, Cambridge, Massachusetts 02138, USA
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12
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Palberg T. Crystallization kinetics of colloidal model suspensions: recent achievements and new perspectives. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2014; 26:333101. [PMID: 25035303 DOI: 10.1088/0953-8984/26/33/333101] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Colloidal model systems allow studying crystallization kinetics under fairly ideal conditions, with rather well-characterized pair interactions and minimized external influences. In complementary approaches experiment, analytic theory and simulation have been employed to study colloidal solidification in great detail. These studies were based on advanced optical methods, careful system characterization and sophisticated numerical methods. Over the last decade, both the effects of the type, strength and range of the pair-interaction between the colloidal particles and those of the colloid-specific polydispersity have been addressed in a quantitative way. Key parameters of crystallization have been derived and compared to those of metal systems. These systematic investigations significantly contributed to an enhanced understanding of the crystallization processes in general. Further, new fundamental questions have arisen and (partially) been solved over the last decade: including, for example, a two-step nucleation mechanism in homogeneous nucleation, choice of the crystallization pathway, or the subtle interplay of boundary conditions in heterogeneous nucleation. On the other hand, via the application of both gradients and external fields the competition between different nucleation and growth modes can be controlled and the resulting microstructure be influenced. The present review attempts to cover the interesting developments that have occurred since the turn of the millennium and to identify important novel trends, with particular focus on experimental aspects.
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Affiliation(s)
- Thomas Palberg
- Institut für Physik, Johannes Gutenberg Universität Mainz, 55099 Mainz, Germany
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13
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Lu PJ, Shutman M, Sloutskin E, Butenko AV. Locating particles accurately in microscope images requires image-processing kernels to be rotationally symmetric. OPTICS EXPRESS 2013; 21:30755-30763. [PMID: 24514652 DOI: 10.1364/oe.21.030755] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Computerized image-analysis routines deployed widely to locate and track the positions of particles in microscope images include several steps where images are convolved with kernels to remove noise. In many common implementations, some kernels are rotationally asymmetric. Here we show that the use of these asymmetric kernels creates significant artifacts, distorting apparent particle positions in a way that gives the artificial appearance of orientational crystalline order, even in such fully-disordered isotropic systems as simple fluids of hard-sphere-like colloids. We rectify this problem by replacing all asymmetric kernels with rotationally-symmetric kernels, which does not impact code performance. We show that these corrected codes locate particle positions properly, restoring measured isotropy to colloidal fluids. We also investigate rapidly-formed colloidal sediments, and with the corrected codes show that these sediments, often thought to be amorphous, may exhibit strong orientational correlations among bonds between neighboring colloidal particles.
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14
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Nigro B, Grimaldi C, Ryser P, Varrato F, Foffi G, Lu PJ. Enhanced tunneling conductivity induced by gelation of attractive colloids. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2013; 87:062312. [PMID: 23848680 DOI: 10.1103/physreve.87.062312] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Revised: 04/04/2013] [Indexed: 06/02/2023]
Abstract
We show that the formation of a gel by conducting colloidal particles leads to a dramatic enhancement in bulk conductivity, due to interparticle electron tunneling, combining predictions from molecular-dynamics simulations with structural measurements in an experimental colloid system. Our results show how colloidal gelation can be used as a general route to huge enhancements of conductivity, and suggest a feasible way for developing cheap materials with novel properties and low metal content.
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Affiliation(s)
- Biagio Nigro
- LPM, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
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15
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Kicheva A, Holtzer L, Wartlick O, Schmidt T, González-Gaitán M. Quantitative imaging of morphogen gradients in Drosophila imaginal discs. Cold Spring Harb Protoc 2013; 2013:387-403. [PMID: 23637364 DOI: 10.1101/pdb.top074237] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Cells at different positions in a developing tissue receive different concentrations of signaling molecules, called morphogens, and this influences their cell fate. Morphogen concentration gradients have been proposed to control patterning as well as growth in many developing tissues. Some outstanding questions about tissue patterning by morphogen gradients are the following: What are the mechanisms that regulate gradient formation and shape? Is the positional information encoded in the gradient sufficiently precise to determine the positions of target gene domain boundaries? What are the temporal dynamics of gradients and how do they relate to patterning and growth? These questions are inherently quantitative in nature and addressing them requires measuring morphogen concentrations in cells, levels of downstream signaling activity, and kinetics of morphogen transport. Here we first present methods for quantifying morphogen gradient shape in which the measurements can be calibrated to reflect actual morphogen concentrations. We then discuss using fluorescence recovery after photobleaching to study the kinetics of morphogen transport at the tissue level. Finally, we present particle tracking as a method to study morphogen intracellular trafficking.
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16
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Bruce MA, Butte MJ. Real-time GPU-based 3D Deconvolution. OPTICS EXPRESS 2013; 21:4766-73. [PMID: 23482010 PMCID: PMC3601650 DOI: 10.1364/oe.21.004766] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Revised: 01/21/2013] [Accepted: 01/31/2013] [Indexed: 05/05/2023]
Abstract
Confocal microscopy is an oft-used technique in biology. Deconvolution of 3D images reduces blurring from out-of-focus light and enables quantitative analyses, but existing software for deconvolution is slow and expensive. We present a parallelized software method that runs within ImageJ and deconvolves 3D images ~100 times faster than conventional software (few seconds per image) by running on a low-cost graphics processor board (GPU). We demonstrate the utility of this software by analyzing microclusters of T cell receptors in the immunological synapse of a CD4 + T cell and dendritic cell. This software provides a low-cost and rapid way to improve the accuracy of 3D microscopic images obtained by any method.
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Affiliation(s)
- Marc A. Bruce
- Stanford Immunology, Stanford University, Stanford, California 94305,
USA
| | - Manish J. Butte
- Stanford Immunology, Stanford University, Stanford, California 94305,
USA
- Department of Pediatrics, Stanford University, Stanford, California 94305
USA
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17
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Caswell TA, Zhang Z, Gardel ML, Nagel SR. Observation and characterization of the vestige of the jamming transition in a thermal three-dimensional system. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2013; 87:012303. [PMID: 23410327 DOI: 10.1103/physreve.87.012303] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2012] [Revised: 11/06/2012] [Indexed: 06/01/2023]
Abstract
We study the dependence on the packing fraction of the pair-correlation function g(r) and particle mobility in a dense three-dimensional packing of soft colloids made of poly N-isopropyl acrylamide (pNIPAM), a thermosensitive gel. We find that g(r) for our samples is qualitatively like that of a liquid at all packing fractions. There is a peak in g(1), the height of the first peak of g(r), as a function of the packing fraction. This peak is identified as a vestige, which remains at finite temperature, of the divergence found at the jamming transition in simulations of soft frictionless spheres at zero temperature. As the density is increased, the particle dynamics slow down and near the packing fraction where there is a peak in g(1) the particles become arrested on the time scale of the experiment.
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Affiliation(s)
- Thomas A Caswell
- The James Franck Institute and Department of Physics, The University of Chicago, Chicago, Illinois 60637, USA
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18
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Cohen AP, Janai E, Rapaport DC, Schofield AB, Sloutskin E. Structure and interactions in fluids of prolate colloidal ellipsoids: Comparison between experiment, theory, and simulation. J Chem Phys 2012; 137:184505. [DOI: 10.1063/1.4765100] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
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19
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Butenko AV, Mogilko E, Amitai L, Pokroy B, Sloutskin E. Coiled to diffuse: Brownian motion of a helical bacterium. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:12941-12947. [PMID: 22891749 DOI: 10.1021/la302056j] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
We employ real-time three-dimensional confocal microscopy to follow the Brownian motion of a fixed helically shaped Leptospira interrogans (LI) bacterium. We extract from our measurements the translational and the rotational diffusion coefficients of this bacterium. A simple theoretical model is suggested, perfectly reproducing the experimental diffusion coefficients, with no tunable parameters. An older theoretical model, where edge effects are neglected, dramatically underestimates the observed rates of translation. Interestingly, the coiling of LI increases its rotational diffusion coefficient by a factor of 5, compared to a (hypothetical) rectified bacterium of the same contour length. Moreover, the translational diffusion coefficients would have decreased by a factor of ~1.5, if LI were rectified. This suggests that the spiral shape of the spirochaete bacteria, in addition to being employed for their active twisting motion, may also increase the ability of these bacteria to explore the surrounding fluid by passive Brownian diffusion.
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Affiliation(s)
- Alexander V Butenko
- Physics Department and Institute for Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan 52900, Israel
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20
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Lu PJ, Giavazzi F, Angelini TE, Zaccarelli E, Jargstorff F, Schofield AB, Wilking JN, Romanowsky MB, Weitz DA, Cerbino R. Characterizing concentrated, multiply scattering, and actively driven fluorescent systems with confocal differential dynamic microscopy. PHYSICAL REVIEW LETTERS 2012; 108:218103. [PMID: 23003305 DOI: 10.1103/physrevlett.108.218103] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2010] [Revised: 02/21/2012] [Indexed: 05/09/2023]
Abstract
We introduce confocal differential dynamic microscopy (ConDDM), a new technique yielding information comparable to that given by light scattering but in dense, opaque, fluorescent samples of micron-sized objects that cannot be probed easily with other existing techniques. We measure the correct wave vector q-dependent structure and hydrodynamic factors of concentrated hard-sphere-like colloids. We characterize concentrated swimming bacteria, observing ballistic motion in the bulk and a new compressed-exponential scaling of dynamics, and determine the velocity distribution; by contrast, near the coverslip, dynamics scale differently, suggesting that bacterial motion near surfaces fundamentally differs from that of freely swimming organisms.
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Affiliation(s)
- Peter J Lu
- Department of Physics and SEAS, Harvard University, Cambridge, Massachusetts 02138, USA
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21
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Fei P, Yu Z, Wang X, Lu PJ, Fu Y, He Z, Xiong J, Huang Y. High dynamic range optical projection tomography (HDR-OPT). OPTICS EXPRESS 2012; 20:8824-8836. [PMID: 22513593 DOI: 10.1364/oe.20.008824] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Traditional optical projection tomography (OPT) acquires a single image at each rotation angle, thereby suffering from limitations in CCD dynamic range; this conventional usage cannot resolve features in samples with highly heterogeneous absorption, such as in small animals with organs of varying size. We present a novel technique, applying multiple-exposure high dynamic range (HDR) imaging to OPT, and demonstrate its ability to resolve fine details in zebrafish embryos, without complicated chemical clearing. We implement the tomographic reconstruction algorithm on the GPU, yielding a performance increase of two orders of magnitude. These features give our method potential application in high-throughput, high-resolution in vivo 3D imaging.
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Affiliation(s)
- Peng Fei
- Biodynamic Optical Imaging Center (BIOPIC), Peking University, Beijing 100871, China
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22
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Muluneh M, Weitz DA. Direct visualization of three-dimensional crystallization behavior in microgels. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2012; 85:021405. [PMID: 22463210 DOI: 10.1103/physreve.85.021405] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2011] [Revised: 12/27/2011] [Indexed: 05/28/2023]
Abstract
We use confocal microscopy to study the three-dimensional (3D) structure of colloidal crystals formed by poly(N-isopropylacrylamide)-co-(acrylic acid) microgels of diameter 1.0-1.5 μm. The confocal images are tracked to locate particle positions in 3D, which are used to compute pair-correlation functions g(r), bond order parameters, and structure factors s(q). We find that the structure remains fcc for a range of charge, size, and concentration of the particles. When the particles are weakly attractive and are at low concentrations, polycrystalline solids result. In addition, owing to the compressibility of the colloids, the crystals display remarkable structural stability when subjected to external stress.
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Affiliation(s)
- Melaku Muluneh
- Department of Physics, Harvard University, Cambridge, Massachusetts 02138, USA.
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23
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Cohen AP, Janai E, Mogilko E, Schofield AB, Sloutskin E. Fluid suspensions of colloidal ellipsoids: direct structural measurements. PHYSICAL REVIEW LETTERS 2011; 107:238301. [PMID: 22182131 DOI: 10.1103/physrevlett.107.238301] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2011] [Indexed: 05/31/2023]
Abstract
A fluid of spheroids, ellipsoids of revolution, is among the simplest models of the disordered matter, where positional and rotational degrees of freedom of the constituent particles are coupled. However, while highly anisometric rods, and hard spheres, were intensively studied in the last decades, the structure of a fluid of spheroids is still unknown. We reconstruct the structure of a simple fluid of spheroids, employing direct confocal imaging of colloids, in three dimensions. The ratio t between the polar axis and the equatorial diameter for both our prolate and oblate spheroids is not far from unity, which gives rise to a delicate interplay between rotations and translations. Strikingly, the measured positional interparticle correlations are significantly stronger than theoretically predicted, indicating that further theoretical attention is required, to fully understand the coupling between translations and rotations in these fundamental fluids.
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Affiliation(s)
- A P Cohen
- Physics Department and Institute for Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan 52900, Israel
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24
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Kamerzell TJ, Esfandiary R, Joshi SB, Middaugh CR, Volkin DB. Protein-excipient interactions: mechanisms and biophysical characterization applied to protein formulation development. Adv Drug Deliv Rev 2011; 63:1118-59. [PMID: 21855584 DOI: 10.1016/j.addr.2011.07.006] [Citation(s) in RCA: 348] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2011] [Revised: 07/19/2011] [Accepted: 07/26/2011] [Indexed: 12/18/2022]
Abstract
The purpose of this review is to demonstrate the critical importance of understanding protein-excipient interactions as a key step in the rational design of formulations to stabilize and deliver protein-based therapeutic drugs and vaccines. Biophysical methods used to examine various molecular interactions between solutes and protein molecules are discussed with an emphasis on applications to pharmaceutical excipients in terms of their effects on protein stability. Key mechanisms of protein-excipient interactions such as electrostatic and cation-pi interactions, preferential hydration, dispersive forces, and hydrogen bonding are presented in the context of different physical states of the formulation such as frozen liquids, solutions, gels, freeze-dried solids and interfacial phenomenon. An overview of the different classes of pharmaceutical excipients used to formulate and stabilize protein therapeutic drugs is also presented along with the rationale for use in different dosage forms including practical pharmaceutical considerations. The utility of high throughput analytical methodologies to examine protein-excipient interactions is presented in terms of expanding formulation design space and accelerating experimental timelines.
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Affiliation(s)
- Tim J Kamerzell
- Cardiovascular Research Institute, University of Kansas Medical Center, Kansas City, KS 66160, USA.
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25
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Jerison ER, Xu Y, Wilen LA, Dufresne ER. Deformation of an elastic substrate by a three-phase contact line. PHYSICAL REVIEW LETTERS 2011; 106:186103. [PMID: 21635105 DOI: 10.1103/physrevlett.106.186103] [Citation(s) in RCA: 142] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2011] [Indexed: 05/30/2023]
Abstract
Young's classic analysis of the equilibrium of a three-phase contact line ignores the out-of-plane component of the liquid-vapor surface tension. While it is expected that this unresolved force is balanced by the elastic response of the solid, a definitive analysis has remained elusive because of an apparent divergence of stress at the contact line. While a number of theories have been presented to cut off the divergence, none of them have provided reasonable agreement with experimental data. We measure surface and bulk deformation of a thin elastic film near a three-phase contact line using fluorescence confocal microscopy. The out-of-plane deformation is well fit by a linear elastic theory incorporating an out-of-plane restoring force due to the surface tension of the solid substrate. This theory predicts that the deformation profile near the contact line is scale-free and independent of the substrate elastic modulus.
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26
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Imaging in-plane and normal stresses near an interface crack using traction force microscopy. Proc Natl Acad Sci U S A 2010; 107:14964-7. [PMID: 20696929 DOI: 10.1073/pnas.1005537107] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Colloidal coatings, such as paint, are all around us. However, we know little about the mechanics of the film-forming process because the composition and properties of drying coatings vary dramatically in space and time. To surmount this challenge, we extend traction force microscopy to quantify the spatial distribution of all three components of the stress at the interface of two materials. We apply this approach to image stress near the tip of a propagating interface crack in a drying colloidal coating and extract the stress intensity factor.
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27
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Yang H. Progress in single-molecule spectroscopy in cells. Curr Opin Chem Biol 2010; 14:3-9. [DOI: 10.1016/j.cbpa.2009.10.015] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2009] [Revised: 10/12/2009] [Accepted: 10/12/2009] [Indexed: 11/26/2022]
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28
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Abstract
Until recently, Brownian motion was seen as an immutable feature of small particles in room-temperature liquids. Molecules, viruses, organelles, and small cells jiggle incessantly due to countless collisions with thermally agitated molecules of solvent. Einstein showed in 1905 that this motion is intimately linked to the tendency of every system to relax toward thermal equilibrium. In recent years, we and others have realized that Brownian motion is not as inescapable as one might think. By tracking the motion of a small particle and applying correction forces to the particle or to the measurement apparatus, one can largely suppress the Brownian motion of particles as small as a few nanometers in diameter, in aqueous solution at room temperature. This new ability to stabilize single molecules has led to a host of studies on topics ranging from the conformational dynamics of DNA to the optical properties of metal nanoparticles. In this review, we outline the physical principles behind suppression of Brownian motion. We discuss the relative merits of several systems that have been implemented. We give examples of studies performed with our anti-Brownian Electrokinetic trap (ABEL trap) as well as other anti-Brownian traps, and we discuss prospects for future research.
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Affiliation(s)
- Alexander P Fields
- Department of Biophysics, Harvard University, Cambridge, Massachusetts, USA
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29
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Perro A, Meng G, Fung J, Manoharan VN. Design and synthesis of model transparent aqueous colloids with optimal scattering properties. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2009; 25:11295-11298. [PMID: 19728724 DOI: 10.1021/la902861x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
We demonstrate the synthesis and self-assembly of colloidal particles with independently controlled diameter and scattering cross section. We show that it is possible to prepare bulk colloidal suspensions that are nearly transparent in water, while the particles themselves can be individually resolved using optical microscopy. These particles may be ideal model colloids for real-space studies of self-assembly in aqueous media. Moreover, they illustrate the degree to which the optical properties of colloids can be engineered through straightforward chemistry.
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Affiliation(s)
- Adeline Perro
- School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, USA
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30
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Gao Y, Kilfoil ML. Accurate detection and complete tracking of large populations of features in three dimensions. OPTICS EXPRESS 2009; 17:4685-704. [PMID: 19293898 DOI: 10.1364/oe.17.004685] [Citation(s) in RCA: 121] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2009] [Accepted: 02/28/2009] [Indexed: 05/23/2023]
Abstract
Localization and tracking of colloidal particles in microscopy images generates the raw data necessary to understand both the dynamics and the mechanical properties of colloidal model systems. Yet, despite the obvious importance of analyzing particle movement in three dimensions (3D), accurate sub-pixel localization of the particles in 3D has received little attention so far. Tracking has been limited by the choice of whether to track all particles in a low-density system, or whether to neglect the most mobile fraction of particles in a dense system. Moreover, assertions are frequently made on the accuracies of methods for locating particles in colloid physics and in biology, and the field of particle locating and tracking can be well-served by quantitative comparison of relative performances. We show that by iterating sub-pixel localization in three dimensions, the centers of particles can be more accurately located in three-dimensions (3D) than with all previous methods by at least half an order of magnitude. In addition, we show that implementing a multi-pass deflation approach, greater fidelity can be achieved in reconstruction of trajectories, once particle positions are known. In general, all future work must defend the accuracy of the particle tracks to be considered reliable. Specifically, other researchers must use the methods presented here (or an alternative whose accuracy can be substantianted) in order for the entire investigation to be considered legitimate, if the basis of the physical argument (in colloids, biology, or any other application) depends on quantitative accuracy of particle positions. We compare our algorithms to other recent and related advances in location/tracking in colloids and in biology, and discuss the relative strengths and weaknesses of all the algorithms in various situations. We carry out performance tests directly comparing the accuracy of our and other 3D methods with simulated data for both location and tracking, and in providing relative performance data, we assess just how accurately software can locate particles. We discuss how our methods, now applied to colloids, could improve the location and tracking of features such as quantum dots in cells.
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Affiliation(s)
- Yongxiang Gao
- Department of Physics, McGill University, Montréal, Canada
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31
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32
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Gelation of particles with short-range attraction. Nature 2008; 453:499-503. [DOI: 10.1038/nature06931] [Citation(s) in RCA: 731] [Impact Index Per Article: 45.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2007] [Accepted: 03/14/2008] [Indexed: 11/09/2022]
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33
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Samsonov D, Elsaesser A, Edwards A, Thomas HM, Morfill GE. High speed laser tomography system. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2008; 79:035102. [PMID: 18377040 DOI: 10.1063/1.2885683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
A high speed laser tomography system was developed capable of acquiring three-dimensional (3D) images of optically thin clouds of moving micron-sized particles. It operates by parallel-shifting an illuminating laser sheet with a pair of galvanometer-driven mirrors and synchronously recording two-dimensional (2D) images of thin slices of the imaged volume. The maximum scanning speed achieved was 120,000 slices/s, sequences of 24 volume scans (up to 256 slices each) have been obtained. The 2D slices were stacked to form 3D images of the volume, then the positions of the particles were identified and followed in the consecutive scans. The system was used to image a complex plasma with particles moving at speeds up to cm/s.
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Affiliation(s)
- D Samsonov
- Department of Electrical Engineering and Electronics, University of Liverpool, Brownlow Hill, L69 3GJ Liverpool, United Kingdom
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34
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News in brief. Nat Methods 2007. [DOI: 10.1038/nmeth0907-685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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