Physics, Department of

Receive updates for this collection

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): 

Toward the Design Principles of Molecular Machines

Peer reviewed: 
Yes, item is peer reviewed.
Date created: 
2017-05-18
Abstract: 

Living things avoid equilibrium using molecular machines. Such microscopic soft-matter objects encounter relatively large friction and fluctuations. We discuss design principles for effective molecular machine operation in this unfamiliar context.

Document type: 
Article
File(s): 

Electrical Conduction and Structure of Copper Atomic Junctions in the Presence of Water Molecules

Peer reviewed: 
Yes, item is peer reviewed.
Abstract: 

We have investigated Cu atomic contacts in the presence of H2O both experimentally and theoretically. The conductance measurements showed the formation of H2O/Cu junctions with a fixed conductance value of around 0.1 G0 (G0 = 2e2/h). These structures were found to be stable and could be stretched over 0.5 nm, indicating the formation of an atomic or molecular chain. In agreement with the experimental findings, theoretical calculations revealed that the conductance of H2O/Cu junctions decreases in stages as the junction is stretched, with the formation of a H2O/Cu atomic chain with a conductance of ca. 0.1 G0 prior to junction rupture. Conversely, in the absence of H2O, the conductance of the Cu junction remains close to 1 G0prior to the junction rupture and abrupt conductance drop.

Document type: 
Article
File(s): 

Probing Long-Range Interactions by Extracting Free Energies From Genome-Wide Chromosome Conformation Capture Data

Peer reviewed: 
Yes, item is peer reviewed.
Date created: 
2015
Abstract: 

Background

A variety of DNA binding proteins are involved in regulating and shaping the packing of chromatin. They aid the formation of loops in the DNA that function to isolate different structural domains. A recent experimental technique, Hi-C, provides a method for determining the frequency of such looping between all distant parts of the genome. Given that the binding locations of many chromatin associated proteins have also been measured, it has been possible to make estimates for their influence on the long-range interactions as measured by Hi-C. However, a challenge in this analysis is the predominance of non-specific contacts that mask out the specific interactions of interest.

Results

We show that transforming the Hi-C contact frequencies into free energies gives a natural method for separating out the distance dependent non-specific interactions. In particular we apply Principal Component Analysis (PCA) to the transformed free energy matrix to identify the dominant modes of interaction. PCA identifies systematic effects as well as high frequency spatial noise in the Hi-C data which can be filtered out. Thus it can be used as a data driven approach for normalizing Hi-C data. We assess this PCA based normalization approach, along with several other normalization schemes, by fitting the transformed Hi-C data using a pairwise interaction model that takes as input the known locations of bound chromatin factors. The result of fitting is a set of predictions for the coupling energies between the various chromatin factors and their effect on the energetics of looping. We show that the quality of the fit can be used as a means to determine how much PCA filtering should be applied to the Hi-C data.

Conclusions

We find that the different normalizations of the Hi-C data vary in the quality of fit to the pairwise interaction model. PCA filtering can improve the fit, and the predicted coupling energies lead to biologically meaningful insights for how various chromatin bound factors influence the stability of DNA loops in chromatin.

Document type: 
Article
File(s): 

Development and Characterization of a Eukaryotic Expression System for Human Type II Procollagen

Peer reviewed: 
Yes, item is peer reviewed.
Date created: 
2015
Abstract: 

Background

Triple helical collagens are the most abundant structural protein in vertebrates and are widely used as biomaterials for a variety of applications including drug delivery and cellular and tissue engineering. In these applications, the mechanics of this hierarchically structured protein play a key role, as does its chemical composition. To facilitate investigation into how gene mutations of collagen lead to disease as well as the rational development of tunable mechanical and chemical properties of this full-length protein, production of recombinant expressed protein is required.

Results

Here, we present a human type II procollagen expression system that produces full-length procollagen utilizing a previously characterized human fibrosarcoma cell line for production. The system exploits a non-covalently linked fluorescence readout for gene expression to facilitate screening of cell lines. Biochemical and biophysical characterization of the secreted, purified protein are used to demonstrate the proper formation and function of the protein. Assays to demonstrate fidelity include proteolytic digestion, mass spectrometric sequence and posttranslational composition analysis, circular dichroism spectroscopy, single-molecule stretching with optical tweezers, atomic-force microscopy imaging of fibril assembly, and transmission electron microscopy imaging of self-assembled fibrils.

Conclusions

Using a mammalian expression system, we produced full-length recombinant human type II procollagen. The integrity of the collagen preparation was verified by various structural and degradation assays. This system provides a platform from which to explore new directions in collagen manipulation.

Document type: 
Article
File(s): 

An Element of Determinism in a Stochastic Flagellar Motor Switch

Peer reviewed: 
Yes, item is peer reviewed.
Date created: 
2015
Abstract: 

Marine bacterium Vibrio alginolyticus uses a single polar flagellum to navigate in an aqueous environment. Similar to Escherichia coli cells, the polar flagellar motor has two states; when the motor is counter-clockwise, the cell swims forward and when the motor is clockwise, the cell swims backward. V. alginolyticus also incorporates a direction randomization step at the start of the forward swimming interval by flicking its flagellum. To gain an understanding on how the polar flagellar motor switch is regulated, distributions of the forward Δf and backward Δb intervals are investigated herein. We found that the steady-state probability density functions, Pf) and Pb), of freely swimming bacteria are strongly peaked at a finite time, suggesting that the motor switch is not Poissonian. The short-time inhibition is sufficiently strong and long lasting, i.e., several hundred milliseconds for both intervals, which is readily observed and characterized. Treating motor reversal dynamics as a first-passage problem, which results from conformation fluctuations of the motor switch, we calculated Pf) and Pb) and found good agreement with the measurements.

Document type: 
Article
File(s):