Physics, Department of

Receive updates for this collection

Effects of Finite and Discrete Sampling and Blur on Microrheology Experiments

Peer reviewed: 
Yes, item is peer reviewed.
Date created: 
2017-12-11
Abstract: 

The frequency-dependent viscous and elastic properties of fluids can be determined from measurements of the thermal fluctuations of a micron-sized particle trapped by optical tweezers. Finite bandwidth and other instrument limitations lead to systematic errors in measurement of the fluctuations. In this work, we numerically represented power spectra of bead position measurements as if collected by two different measurement devices: a quadrant photodiode, which measures the deflection of the trapping laser; and a high-speed camera, which images the trapped bead directly. We explored the effects of aliasing, camera blur, sampling frequency, and measurement time. By comparing the power spectrum, complex response function, and the complex shear modulus with the ideal values, we found that the viscous and elastic properties inferred from the data are affected by the instrument limitations of each device. We discuss how these systematic effects might affect experimental results from microrheology measurements and suggest approaches to reduce discrepancies.

Document type: 
Article
File(s): 

Dense Neural Networks for Predicting Chromatin Conformation

Peer reviewed: 
Yes, item is peer reviewed.
Date created: 
2018-10-11
Abstract: 

Background  DNA inside eukaryotic cells wraps around histones to form the 11nm chromatin fiber that can further fold into higher-order DNA loops, which may depend on the binding of architectural factors. Predicting how the DNA will fold given a distribution of bound factors, here viewed as a type of sequence, is currently an unsolved problem and several heterogeneous polymer models have shown that many features of the measured structure can be reproduced from simulations. However a model that determines the optimal connection between sequence and structure and that can rapidly assess the effects of varying either one is still lacking.

Results  Here we train a dense neural network to solve for the local folding of chromatin, connecting structure, represented as a contact map, to a sequence of bound chromatin factors. The network includes a convolutional filter that compresses the large number of bound chromatin factors into a single 1D sequence representation that is optimized for predicting structure. We also train a network to solve the inverse problem, namely given only structural information in the form of a contact map, predict the likely sequence of chromatin states that generated it.

Conclusions  By carrying out sensitivity analysis on both networks, we are able to highlight the importance of chromatin contexts and neighborhoods for regulating long-range contacts, along with critical alterations that affect contact formation. Our analysis shows that the networks have learned physical insights that are informative and intuitive about this complex polymer problem.

Document type: 
Article
File(s): 

A Maximum-Entropy Model for Predicting Chromatin Contacts

Peer reviewed: 
Yes, item is peer reviewed.
Date created: 
2018-02-05
Abstract: 

The packaging of DNA inside a nucleus shows complex structure stabilized by a host of DNA-bound factors. Both the distribution of these factors and the contacts between different genomic locations of the DNA can now be measured on a genome-wide scale. This has advanced the development of models aimed at predicting the conformation of DNA given only the locations of bound factors—the chromatin folding problem. Here we present a maximum-entropy model that is able to predict a contact map representation of structure given a sequence of bound factors. Non-local effects due to the sequence neighborhood around contacting sites are found to be important for making accurate predictions. Lastly, we show that the model can be used to infer a sequence of bound factors given only a measurement of structure. This opens up the possibility for efficiently predicting sequence regions that may play a role in generating cell-type specific structural differences.

Document type: 
Article
File(s): 

DNA Segregation Under Par Protein Control

Peer reviewed: 
Yes, item is peer reviewed.
Date created: 
2019-07-18
Abstract: 

The spatial organization of DNA is mediated by the Par protein system in some bacteria. ParB binds specifically to the parS sequence on DNA and orchestrates its motion by interacting with ParA bound to the nucleoid. In the case of plasmids, a single ParB bound plasmid is observed to execute oscillations between cell poles while multiple plasmids eventually settle at equal distances from each other along the cell’s length. While the potential mechanism underlying the ParA-ParB interaction has been discussed, it remains unclear whether ParB-complex oscillations are stable limit cycles or merely decaying transients to a fixed point. How are dynamics affected by substrate length and the number of complexes? We present a deterministic model for ParA-ParB driven DNA segregation where the transition between stable arrangements and oscillatory behaviour depends only on five parameters: ParB-complex number, substrate length, ParA concentration, ParA hydrolysis rate and the ratio of the lengthscale over which the ParB complex stimulates ParA hydrolysis to the lengthscale over which ParA interacts with the ParB complex. When the system is buffered and the ParA rebinding rate is constant we find that ParB-complex dynamics is independent of substrate length and complex number above a minimum system size. Conversely, when ParA resources are limited, we find that changing substrate length and increasing complex number leads to counteracting mechanisms that can both generate or subdue oscillatory dynamics. We argue that cells may be poised near a critical level of ParA so that they can transition from oscillatory to fixed point dynamics as the cell cycle progresses so that they can both measure their size and faithfully partition their genetic material. Lastly, we show that by modifying the availability of ParA or depletion zone size, we can capture some of the observed differences in ParB-complex positioning between replicating chromosomes in B. subtilis cells and low-copy plasmids in E. coli cells.

Document type: 
Article
File(s): 

Improved Characterization of Hydrogen Fuel Cell Membranes

Author: 
Peer reviewed: 
No, item is not peer reviewed.
Date created: 
2019-05-05
Abstract: 

I characterized the morphology of a hydrogen fuel cell membrane commercially known as Nafion. First generation Nafion (N112/N115) was compared with the second generation (N211) at various temperatures and humidities to examine their structural differences. The membranes were analyzed in a new humidity- and temperature-controlled chamber (Xenocs) using small angle X-ray scattering (SAXS) at temperatures ranging from 30-80C and relative humidities (RH) between 30-90%. The Kapton chamber windows were characterized to allow for proper background subtraction of Kapton intensity profiles, and folded and not folded membrane samples were compared to determine an easier method for mounting. Equilibration time for changes in the Nafion structure after an RH change of 30 and 40% were observed to be of the order of 30 minutes. The membrane profiles at different RH were fit to a multi-peak pseudo-Voigt function with a constant offset and negative power law at low Q (reciprocal space) values, with a clear ionomer peak (0.2 A^-1) appearing above 40% RH for N115 and 30% RH for N112 and N211. The membranes were also analyzed using dynamic vapour sorption (DVS) at 80C; N211 showed a significantly higher increase in water uptake than N112/N115.

Document type: 
Report
File(s): 

Antihydrogen Accumulation for Fundamental Symmetry Tests

Peer reviewed: 
Yes, item is peer reviewed.
Date created: 
2017-09-25
Abstract: 

Antihydrogen, a positron bound to an antiproton, is the simplest anti-atom. Its structure and properties are expected to mirror those of the hydrogen atom. Prospects for precision comparisons of the two, as tests of fundamental symmetries, are driving a vibrant programme of research. In this regard, a limiting factor in most experiments is the availability of large numbers of cold ground state antihydrogen atoms. Here, we describe how an improved synthesis process results in a maximum rate of 10.5 ± 0.6 atoms trapped and detected per cycle, corresponding to more than an order of magnitude improvement over previous work. Additionally, we demonstrate how detailed control of electron, positron and antiproton plasmas enables repeated formation and trapping of antihydrogen atoms, with the simultaneous retention of atoms produced in previous cycles. We report a record of 54 detected annihilation events from a single release of the trapped anti-atoms accumulated from five consecutive cycles.

Document type: 
Article
File(s): 

Morphology of Anion-Conducting Ionenes Investigated by X-ray Scattering and Simulation

Peer reviewed: 
Yes, item is peer reviewed.
Date created: 
2018-01-24
Abstract: 

We have studied the morphology of a novel series of benzimidazole-based ionenes, methylated poly(hexamethyl-p-terphenylbenzimidazolium) (HMT-PMBI), in halide form. Materials with anion-exchange capacities ranging from 0 to 2.5 mequiv/g were studied. X-ray scattering reveals three length scales in the materials: ion–polymer spacing (4 Å), polymer–polymer interchain spacing (6 Å), and an intrachain repeat distance (20 Å). No long-range structure is apparent above the monomer length, which is rare in ion-conducting polymer membranes. In preliminary molecular dynamics simulations, water molecules were observed forming chains between ions, even at a modest level of hydration, providing an interpenetrating network where conductivity can occur.

Document type: 
Article

Effective Dissipation: Breaking Time-Reversal Symmetry in Driven Microscopic Energy Transmission

Peer reviewed: 
Yes, item is peer reviewed.
Date created: 
2016-09-30
Abstract: 

At molecular scales, fluctuations play a significant role and prevent biomolecular processes from always proceeding in a preferred direction, raising the question of how limited amounts of free energy can be dissipated to obtain directed progress. We examine the system and process characteristics that efficiently break time-reversal symmetry at fixed energy loss; in particular for a simple model of a molecular machine, an intermediate energy barrier produces unusually high asymmetry for a given dissipation. We relate the symmetry-breaking factors found in this model to recent observations of biomolecular machines.

Document type: 
Article
File(s): 

Allocating Dissipation Across a Molecular Machine Cycle to Maximize Flux

Peer reviewed: 
Yes, item is peer reviewed.
Date created: 
2017-10-17
Abstract: 

Biomolecular machines consume free energy to break symmetry and make directed progress. Nonequilibrium ATP concentrations are the typical free energy source, with one cycle of a molecular machine consuming a certain number of ATP, providing a fixed free energy budget. Since evolution is expected to favor rapid-turnover machines that operate efficiently, we investigate how this free energy budget can be allocated to maximize flux. Unconstrained optimization eliminates intermediate metastable states, indicating that flux is enhanced in molecular machines with fewer states. When maintaining a set number of states, we show that—in contrast to previous findings—the flux-maximizing allocation of dissipation is not even. This result is consistent with the coexistence of both “irreversible” and reversible transitions in molecular machine models that successfully describe experimental data, which suggests that, in evolved machines, different transitions differ significantly in their dissipation.

Document type: 
Article

Tunable Magnetization and Damping of Sputter-Deposited, Exchange Coupled Py|Fe Bilayers

Peer reviewed: 
Yes, item is peer reviewed.
Date created: 
2017-03
Abstract: 

We report on magnetic damping of exchange coupled, polycrystalline Py(Ni80Fe20)|Fe and Fe|Py bilayers, prepared by sputter-deposition on an amorphous 3nm Ta seed layer. FMR measurements are performed on varying thicknesses of the individual Py and Fe layers while keeping the total bilayer structure thickness fixed. When Fe is grown directly on Ta, there is large magnetic inhomogeneity and damping. However, when a Py layer is deposited between Fe and Ta, both the magnetic inhomogeneity and damping significantly decrease even if Fe is covered by Ta. The intrinsic damping of the Ta|Py|Fe film can be further lowered by increasing the Fe to Py ratio. SQUID measurements show a linear increase in saturation magnetization with increasing ratio of Fe to Py. A combination of in-plane and out-of-plane X-ray diffraction measurements show that Py is textured along the ⟨111⟩ directions and Fe is textured along the ⟨110⟩, with Fe texture significantly improving if it is deposited on Ta|Py instead of Ta. By improving the texture of Fe by introducing a thin Py layer between Fe and Ta, one can grow Fe thin films with zero in-plane anisotropy, tunable magnetic moment, and low magnetic damping, approaching that of the best single crystal Fe.

Document type: 
Article
File(s):