| 1. |
- Iarko, V., et al.
(författare)
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Extension of nanoconfined DNA: Quantitative comparison between experiment and theory
- 2015
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Ingår i: Physical Review E (Statistical, Nonlinear, and Soft Matter Physics). - 1539-3755 .- 1550-2376. ; 92:6, s. Art. Nr. 062701-
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Tidskriftsartikel (refereegranskat)abstract
- The extension of DNA confined to nanochannels has been studied intensively and in detail. However, quantitative comparisons between experiments and model calculations are difficult because most theoretical predictions involve undetermined prefactors, and because the model parameters (contour length, Kuhn length, effective width) are difficult to compute reliably, leading to substantial uncertainties. Here we use a recent asymptotically exact theory for the DNA extension in the "extended de Gennes regime" that allows us to compare experimental results with theory. For this purpose, we performed experiments measuring the mean DNA extension and its standard deviation while varying the channel geometry, dye intercalation ratio, and ionic strength of the buffer. The experimental results agree very well with theory at high ionic strengths, indicating that the model parameters are reliable. At low ionic strengths, the agreement is less good. We discuss possible reasons. In principle, our approach allows us to measure the Kuhn length and the effective width of a single DNA molecule and more generally of semiflexible polymers in solution.
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| 2. |
- Alhassid, Y, et al.
(författare)
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Fano interference and cross-section fluctuations in molecular photodissociation
- 2006
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Ingår i: Physical Review A. - 1050-2947. ; 73
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Tidskriftsartikel (refereegranskat)abstract
- We derive an expression for the total photodissociation cross section of a molecule incorporating both direct and indirect processes that proceed through excited resonances, and show that it exhibits generalized Beutler-Fano line shapes. Assuming that the closed system can be modeled by random-matrix theory, we derive the statistical properties of the photodissociation cross section and find that they are significantly affected by the direct processes. In the limit of isolated resonances, we find that direct processes suppress the correlation hole of the cross-section autocorrelation function and lead to a maximum in the cross-section distribution.
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| 3. |
- Alizadehheidari, Mohammadreza, 1987, et al.
(författare)
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Nanoconfined Circular and Linear DNA: Equilibrium Conformations and Unfolding Kinetics
- 2015
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Ingår i: Macromolecules. - : American Chemical Society (ACS). - 0024-9297 .- 1520-5835. ; 48:3, s. 871-878
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Tidskriftsartikel (refereegranskat)abstract
- Studies of circular DNA confined to nanofluidic channels are relevant both from a fundamental polymer-physics perspective and due to the importance of circular DNA molecules in vivo. We here observe the unfolding of confined DNA from the circular to linear configuration as a light-induced double-strand break occurs, characterize the dynamics, and compare the equilibrium conformational statistics of linear and circular configurations. This is important because it allows us to determine to what extent existing statistical theories describe the extension of confined circular DNA. We find that the ratio of the extensions of confined linear and circular DNA configurations increases as the buffer concentration decreases. The experimental results fall between theoretical predictions for the extended de Gennes regime at weaker confinement and the Odijk regime at stronger confinement. We show that it is possible to directly distinguish between circular and linear DNA molecules by measuring the emission intensity from the DNA. Finally, we determine the rate of unfolding and show that this rate is larger for more confined DNA, possibly reflecting the corresponding larger difference in entropy between the circular and linear configurations.
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| 4. |
- Alizadehheidari, Mohammadreza, et al.
(författare)
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Nanoconfined Circular DNA
- 2014
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Ingår i: Biophysical Journal. - : Elsevier BV. - 0006-3495 .- 1542-0086. ; 106:2, s. 274A-274A
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- Nanofluidic channels have become a versatile tool to manipulate single DNA molecules. They allow investigation of confined single DNA molecules from a fundamental polymer physics perspective as well as for example in DNA barcoding techniques.
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| 5. |
- Alizadehheidari, Mohammadreza, 1987, et al.
(författare)
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Unfolding of nanoconfined circular DNA
- 2015
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Ingår i: BIOPHYSICAL JOURNAL. - : Elsevier BV. - 0006-3495 .- 1542-0086. ; 108:2 Supplement 1, s. 231A-231A
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
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| 6. |
- Almondo, Gino, et al.
(författare)
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Intrinsic viscosity of a suspension of weakly Brownian ellipsoids in shear
- 2018
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Ingår i: Physical Review Fluids. - 2469-990X. ; 3:6
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Tidskriftsartikel (refereegranskat)abstract
- We analyze the angular dynamics of triaxial ellipsoids in a shear flow subject to weak thermal noise. By numerically integrating an overdamped angular Langevin equation, we find the steady angular probability distribution for a range of triaxial particle shapes. From this distribution we compute the intrinsic viscosity of a dilute suspension of triaxial particles. We determine how the viscosity depends on particle shape in the limit of weak thermal noise. While the deterministic angular dynamics depends very sensitively on particle shape, we find that the shape dependence of the intrinsic viscosity is weaker, in general, and that suspensions of rodlike particles are the most sensitive to breaking of axisymmetry. The intrinsic viscosity of a dilute suspension of triaxial particles is smaller than that of a suspension of axisymmetric particles with the same volume and the same ratio of major to minor axis lengths.
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| 7. |
- Andersson, Björn, et al.
(författare)
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Advective collisions
- 2007
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Ingår i: Europhysics Letters. - : IOP Publishing. - 0295-5075 .- 1286-4854. ; 80
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Tidskriftsartikel (refereegranskat)
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| 8. |
- Arvedson, Erik, et al.
(författare)
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Staggered ladder spectra.
- 2006
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Ingår i: Physical review letters. - 0031-9007. ; 96:3
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Tidskriftsartikel (refereegranskat)abstract
- We exactly solve a Fokker-Planck equation by determining its eigenvalues and eigenfunctions: we construct nonlinear second-order differential operators which act as raising and lowering operators, generating ladder spectra for the odd- and even-parity states. The ladders are staggered: the odd-even separation differs from even-odd. The Fokker-Planck equation corresponds, in the limit of weak damping, to a generalized Ornstein-Uhlenbeck process where the random force depends upon position as well as time. The process describes damped stochastic acceleration, and exhibits anomalous diffusion at short times and a stationary non-Maxwellian momentum distribution.
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| 9. |
- Balabanov, Oleksandr, et al.
(författare)
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Bayesian Posterior Approximation With Stochastic Ensembles
- 2023
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Ingår i: Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition. - 1063-6919. - 9798350301298 ; 2023-June, s. 13701-13711
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Konferensbidrag (refereegranskat)abstract
- We introduce ensembles of stochastic neural networks to approximate the Bayesian posterior, combining stochastic methods such as dropout with deep ensembles. The stochas-tic ensembles are formulated as families of distributions and trained to approximate the Bayesian posterior with variational inference. We implement stochastic ensembles based on Monte Carlo dropout, DropConnect and a novel non-parametric version of dropout and evaluate them on a toy problem and CIFAR image classification. For both tasks, we test the quality of the posteriors directly against Hamil-tonian Monte Carlo simulations. Our results show that stochastic ensembles provide more accurate posterior esti-mates than other popular baselines for Bayesian inference.
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| 10. |
- Bec, J., et al.
(författare)
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Statistical Models for the Dynamics of Heavy Particles in Turbulence
- 2024
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Ingår i: ANNUAL REVIEW OF FLUID MECHANICS. - 0066-4189 .- 1545-4479. ; 56, s. 189-213
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Forskningsöversikt (refereegranskat)abstract
- When very small particles are suspended in a fluid in motion, they tend to follow the flow. How such tracer particles are mixed, transported, and dispersed by turbulent flow has been successfully described by statistical models. Heavy particles, with mass densities larger than that of the carrying fluid, can detach from the flow. This results in preferential sampling, small-scale fractal clustering, and large relative velocities. To describe these effects of particle inertia, one must consider both particle positions and velocities in phase space. In recent years, statistical phase-space models have significantly contributed to our understanding of inertial-particle dynamics in turbulence. These models help to identify the key mechanisms and nondimensional parameters governing the particle dynamics and have made qualitative and, in some cases, quantitative predictions. This article reviews statistical phase-space models for the dynamics of small, yet heavy, spherical particles in turbulence. We evaluate their effectiveness by comparing their predictions with results from numerical simulations and laboratory experiments, and we summarize their successes and failures.
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