Physics, Department of

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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
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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
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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
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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
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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): 

Operational Principles for the Dynamics of the In Vitro ParA-ParB System

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

In many bacteria the ParA-ParB protein system is responsible for actively segregating DNA during replication. ParB proteins move by interacting with DNA bound ParA-ATP, stimulating their unbinding by catalyzing hydrolysis, that leads to rectified motion due to the creation of a wake of depleted ParA. Recent in vitro experiments have shown that a ParB covered magnetic bead can move with constant speed over a DNA covered substrate that is bound by ParA. It has been suggested that the formation of a gradient in ParA leads to diffusion-ratchet like motion of the ParB bead but how it forms and generates a force is still a matter of exploration. Here we develop a deterministic model for the in vitro ParA-ParB system and show that a ParA gradient can spontaneously form due to any amount of initial spatial noise in bound ParA. The speed of the bead is independent of this noise but depends on the ratio of the range of ParA-ParB force on the bead to that of removal of surface bound ParA by ParB. We find that at a particular ratio the speed attains a maximal value. We also consider ParA rebinding (including cooperativity) and ParA surface diffusion independently as mechanisms for ParA recovery on the surface. Depending on whether the DNA covered surface is undersaturated or saturated with ParA, we find that the bead can accelerate persistently or potentially stall. Our model highlights key requirements of the ParA-ParB driving force that are necessary for directed motion in the in vitro system that may provide insight into the in vivo dynamics of the ParA-ParB system.

Document type: 
Article
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Does the Earth's Magnetic Field Serve as a Reference for Alignment of the Honeybee Waggle Dance?

Peer reviewed: 
Yes, item is peer reviewed.
Date created: 
2014-12-26
Abstract: 

The honeybee (Apis mellifera) waggle dance, which is performed inside the hive by forager bees, informs hive mates about a potent food source, and recruits them to its location. It consists of a repeated figure-8 pattern: two oppositely directed turns interspersed by a short straight segment, the “waggle run”. The waggle run consists of a single stride emphasized by lateral waggling motions of the abdomen. Directional information pointing to a food source relative to the sun's azimuth is encoded in the angle between the waggle run line and a reference line, which is generally thought to be established by gravity. Yet, there is tantalizing evidence that the local (ambient) geomagnetic field (LGMF) could play a role. We tested the effect of the LGMF on the recruitment success of forager bees by placing observation hives inside large Helmholtz coils, and then either reducing the LGMF to 2% or shifting its apparent declination. Neither of these treatments reduced the number of nest mates that waggle dancing forager bees recruited to a feeding station located 200 m north of the hive. These results indicate that the LGMF does not act as the reference for the alignment of waggle-dancing bees.

Document type: 
Article
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Microrheological Characterization of Collagen Systems: From Molecular Solutions to Fibrillar Gels

Peer reviewed: 
Yes, item is peer reviewed.
Date created: 
2013
Abstract: 

Collagen is the most abundant protein in the extracellular matrix (ECM), where its structural organization conveys mechanical information to cells. Using optical-tweezers-based microrheology, we investigated mechanical properties both of collagen molecules at a range of concentrations in acidic solution where fibrils cannot form and of gels of collagen fibrils formed at neutral pH, as well as the development of microscale mechanical heterogeneity during the self-assembly process. The frequency scaling of the complex shear modulus even at frequencies of ~10 kHz was not able to resolve the flexibility of collagen molecules in acidic solution. In these solutions, molecular interactions cause significant transient elasticity, as we observed for 5 mg/ml solutions at frequencies above ~200 Hz. We found the viscoelasticity of solutions of collagen molecules to be spatially homogeneous, in sharp contrast to the heterogeneity of self-assembled fibrillar collagen systems, whose elasticity varied by more than an order of magnitude and in power-law behavior at different locations within the sample. By probing changes in the complex shear modulus over 100-minute timescales as collagen self-assembled into fibrils, we conclude that microscale heterogeneity appears during early phases of fibrillar growth and continues to develop further during this growth phase. Experiments in which growing fibrils dislodge microspheres from an optical trap suggest that fibril growth is a force-generating process. These data contribute to understanding how heterogeneities develop during self-assembly, which in turn can help synthesis of new materials for cellular engineering.

Document type: 
Article
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