# Biological Physics

## New submissions

[ total of 16 entries: 1-16 ]
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### New submissions for Tue, 20 Mar 18

[1]
Title: Actin filaments growing against an elastic membrane: Effect of membrane tension
Journal-ref: Physical Review E, vol. 97, 032408 (2018)
Subjects: Biological Physics (physics.bio-ph); Soft Condensed Matter (cond-mat.soft); Statistical Mechanics (cond-mat.stat-mech)

We study the force generation by a set of parallel actin filaments growing against an elastic membrane. The elastic membrane tries to stay flat and any deformation from this flat state, either caused by thermal fluctuations or due to protrusive polymerization force exerted by the filaments, costs energy. We study two lattice models to describe the membrane dynamics. In one case, the energy cost is assumed to be proportional to the absolute magnitude of the height gradient (gradient model) and in the other case it is proportional to the square of the height gradient (Gaussian model). For the gradient model we find that the membrane velocity is a non-monotonic function of the elastic constant $\mu$, and reaches a peak at $\mu=\mu^\ast$. For $\mu < \mu^\ast$ the system fails to reach a steady state and the membrane energy keeps increasing with time. For the Gaussian model, the system always reaches a steady state and the membrane velocity decreases monotonically with the elastic constant $\nu$ for all nonzero values of $\nu$. Multiple filaments give rise to protrusions at different regions of the membrane and the elasticity of the membrane induces an effective attraction between the two protrusions in the Gaussian model which causes the protrusions to merge and a single wide protrusion is present in the system. In both the models, the relative time-scale between the membrane and filament dynamics plays an important role in deciding whether the shape of elasticity-velocity curve is concave or convex. Our numerical simulations agree reasonably well with our analytical calculations.

[2]
Title: Charge migration mechanisms in the DNA at finite temperature revisited; from quasi-ballistic to subdiffusive transport
Subjects: Biological Physics (physics.bio-ph); Mesoscale and Nanoscale Physics (cond-mat.mes-hall)

Various charge migration mechanisms in the DNA are studied within the framework of the Peyrard-Bishop-Holstein model which has been widely used to address charge dynamics in this macromolecule. To analyze these mechanisms we consider characteristic size and time scales of the fluctuations of the electronic and vibrational subsystems. It is shown, in particular, that due to substantial differences in these timescales polaron formation is unlikely within a broad range of temperatures. We demonstrate that at low temperatures electronic transport can be quasi-ballistic. For high temperatures, we propose an alternative to polaronic charge migration mechanism: the fluctuation-assisted one, in which the electron dynamics is governed by relatively slow fluctuations of the vibrational subsystem. We argue also that the discussed methods and mechanisms can be relevant for other organic macromolecular systems, such as conjugated polymers and molecular aggregates.

[3]
Title: Optically resolving the dynamic walking of a plasmonic walker couple
Journal-ref: Nano Letters 15, 8392 (2015)
Subjects: Biological Physics (physics.bio-ph)

Deterministic placement and dynamic manipulation of individual plasmonic nanoparticles with nanoscale precision feature an important step towards active nanoplasmonic devices with prescribed levels of performance and functionalities at optical frequencies. In this Letter, we demonstrate a plasmonic walker couple system, in which two gold nanorod walkers can independently or simultaneously perform stepwise walking powered by DNA hybridization along the same DNA origami track. We utilize optical spectroscopy to resolve such dynamic walking with nanoscale steps well below the optical diffraction limit. We also show that the number of walkers and the optical response of the system can be correlated. Our studies exemplify the power of plasmonics, when integrated with DNA nanotechnology for realization of advanced artificial nanomachinery with tailored optical functionalities.

[4]
Title: Plasmonic Toroidal Metamolecules Assembled by DNA Origami
Journal-ref: J. Am. Chem. Soc. 138, 5495 (2016)
Subjects: Biological Physics (physics.bio-ph); Soft Condensed Matter (cond-mat.soft)

We demonstrate hierarchical assembly of plasmonic toroidal metamolecules, which exhibit tailored optical activity in the visible spectral range. Each metamolecule consists of four identical origami-templated helical building blocks. Such toroidal metamolecules show stronger chiroptical response than monomers and dimers of the helical building blocks. Enantiomers of the plasmonic structures yield opposite circular dichroism spectra. The experimental results agree well with the theoretical simulations. We also demonstrate that given the circular symmetry of the structures, distinct chiroptical response along their axial orientation can be uncovered via simple spin-coating of the metamolecules on substrates. Our work provides a new strategy to create plasmonic chiral platforms with sophisticated nanoscale architectures for potential applications such as chiral sensing using chemically-based assembly systems.

[5]
Title: DNA nanotechnology-enabled chiral plasmonics: from static to dynamic
Journal-ref: Acc. Chem. Res. 50, 2906 (2017)
Subjects: Biological Physics (physics.bio-ph); Soft Condensed Matter (cond-mat.soft)

In this Account, we discuss a variety of static and dynamic chiral plasmonic nanostructures enabled by DNA nanotechnology. In the category of static plasmonic systems, we first show chiral plasmonic nanostructures based on spherical AuNPs, including plasmonic helices, toroids, and tetramers. To enhance the CD responses, anisotropic gold nanorods with larger extinction coefficients are utilized to create chiral plasmonic crosses and helical superstructures. Next, we highlight the inevitable evolution from static to dynamic plasmonic systems along with the fast development of this interdisciplinary field. Several dynamic plasmonic systems are reviewed according to their working mechanisms.

[6]
Title: Quantized Dehydration and the Determinants of Selectivity in the NaChBac Bacterial Sodium Channel
Comments: 13 pages 7 figure + Supplemental Information
Subjects: Biological Physics (physics.bio-ph); Biomolecules (q-bio.BM)

A discrete electrostatic/diffusion model has been developed to describe the selective permeation of ion channels, based on ionic Coulomb blockade (ICB) and quantised dehydration (QD). It has been applied to describe selectivity phenomena measured in the bacterial NaChBac sodium channel and some of its mutants. Site-directed mutagenesis and the whole-cell patch-clamp technique were used to investigate how the value $Q_f$ of the fixed charge at the selectivity filter (SF) affected both valence and alike-charge selectivity. The new ICB/QD model predicts that increasing ${Q_f}$ should lead to a shift of selectivity sequences towards larger ion sizes and charges, a result that agrees with the present experiments and with earlier work. Comparison of the model with experimental data provides evidence for an {\it effective charge} $Q_f^*$ at the SF that is smaller in magnitude than the nominal $Q_f$ corresponding to the charge on the isolated protein residues. Furthermore, $Q_f^*$ was different for aspartate and glutamate charged rings and also depended on their position within the SF. It is suggested that protonation of the residues within the restricted space is an important factor in significantly reducing the effective charge of the EEEE ring. Values of $Q_f^*$ derived from experiments on the anomalous mole fraction effect (AMFE) agree well with expectations based on the ICB/QD model and have led to the first clear demonstration of the expected ICB oscillations in Ca$^{2+}$ conduction as a function of the fixed charge. Pilot studies of the dependence of Ca$^{2+}$ conduction on pH are consistent with the predictions of the model.

### Cross-lists for Tue, 20 Mar 18

[7]  arXiv:1803.06410 (cross-list from q-bio.QM) [pdf, other]
Title: Accurate evaluation of size and refractive index for spherical objects in quantitative phase imaging
Comments: 14 pages, 10 figures, 1 table
Subjects: Quantitative Methods (q-bio.QM); Biological Physics (physics.bio-ph)

Measuring the average refractive index (RI) of spherical objects, such as suspended cells, in quantitative phase imaging (QPI) requires a decoupling of RI and size from the QPI data. This has been commonly achieved by determining the object's radius with geometrical approaches, neglecting light-scattering. Here, we present a novel QPI fitting algorithm that reliably uncouples the RI using Mie theory and a semi-analytical, corrected Rytov approach. We assess the range of validity of this algorithm in silico and experimentally investigate various objects (oil and protein droplets, microgel beads, cells) and noise conditions. In addition, we provide important practical cues for future studies in cell biology.

[8]  arXiv:1803.06425 (cross-list from cond-mat.soft) [pdf, other]
Title: Reinforcement Learning of Artificial Microswimmers
Subjects: Soft Condensed Matter (cond-mat.soft); Biological Physics (physics.bio-ph)

The behavior of living systems is based on the experience they gained through their interactions with the environment [1]. This experience is stored in the complex biochemical networks of cells and organisms to provide a relationship between a sensed situation and what to do in this situation [2-4]. An implementation of such processes in artificial systems has been achieved through different machine learning algorithms [5, 6]. However, for microscopic systems such as artificial microswimmers which mimic propulsion as one of the basic functionalities of living systems [7, 8] such adaptive behavior and learning processes have not been implemented so far. Here we introduce machine learning algorithms to the motion of artificial microswimmers with a hybrid approach. We employ self-thermophoretic artificial microswimmers in a real world environment [9, 10] which are controlled by a real-time microscopy system to introduce reinforcement learning [11-13]. We demonstrate the solution of a standard problem of reinforcement learning - the navigation in a grid world. Due to the size of the microswimmer, noise introduced by Brownian motion if found to contribute considerably to both the learning process and the actions within a learned behavior. We extend the learning process to multiple swimmers and sharing of information. Our work represents a first step towards the integration of learning strategies into microsystems and provides a platform for the study of the emergence of adaptive and collective behavior.

[9]  arXiv:1803.06449 (cross-list from physics.chem-ph) [pdf, other]
Title: Note: Variational Encoding of Protein Dynamics Benefits from Maximizing Latent Autocorrelation
Subjects: Chemical Physics (physics.chem-ph); Learning (cs.LG); Biological Physics (physics.bio-ph); Machine Learning (stat.ML)

As deep Variational Auto-Encoder (VAE) frameworks become more widely used for modeling biomolecular simulation data, we emphasize the capability of the VAE architecture to concurrently maximize the timescale of the latent space while inferring a reduced coordinate, which assists in finding slow processes as according to the variational approach to conformational dynamics. We additionally provide evidence that the VDE framework (Hern\'{a}ndez et al., 2017), which uses this autocorrelation loss along with a time-lagged reconstruction loss, obtains a variationally optimized latent coordinate in comparison with related loss functions. We thus recommend leveraging the autocorrelation of the latent space while training neural network models of biomolecular simulation data to better represent slow processes.

[10]  arXiv:1803.06544 (cross-list from cond-mat.soft) [pdf, ps, other]
Title: Long ligands reinforce biological adhesion under shear flow
Subjects: Soft Condensed Matter (cond-mat.soft); Biological Physics (physics.bio-ph); Cell Behavior (q-bio.CB)

In the present work the computer modelling was used to show that longer ligands allow biological cells (e.g. blood platelets) to withstand stronger flows after their adhesion to solid walls. Mechanistic model of polymer-mediated ligand-receptor adhesion between a microparticle (cell) and a flat wall was developed. Theoretical threshold between adherent and non-adherent regimes was derived analytically and approved by the simulations. These results lead to deeper understanding of numerous biophysical processes, e.g. arterial thrombosis, and to the design of new biomimetic colloid-polymer systems.

### Replacements for Tue, 20 Mar 18

[11]  arXiv:1703.04401 (replaced) [pdf, other]
Title: Soft inclusion in a confined fluctuating active gel
Journal-ref: Physical Review E, 97, 032602 (2018)
Subjects: Biological Physics (physics.bio-ph); Soft Condensed Matter (cond-mat.soft); Statistical Mechanics (cond-mat.stat-mech)
[12]  arXiv:1710.01954 (replaced) [pdf, ps, other]
Title: Actuated rheology of magnetic micro-swimmers suspensions : emergence of motor and brake states
Comments: 10 pages, 6 figures, accepted in PRFluids
Subjects: Biological Physics (physics.bio-ph); Soft Condensed Matter (cond-mat.soft); Fluid Dynamics (physics.flu-dyn)
[13]  arXiv:1607.04478 (replaced) [pdf, ps, other]
Title: Viscosity and effective temperature of an active dense system of self-propelled particles
Subjects: Soft Condensed Matter (cond-mat.soft); Statistical Mechanics (cond-mat.stat-mech); Biological Physics (physics.bio-ph)
[14]  arXiv:1708.00165 (replaced) [pdf, other]
Title: Ordering dynamics of self-propelled particles in an inhomogeneous medium
Subjects: Statistical Mechanics (cond-mat.stat-mech); Soft Condensed Matter (cond-mat.soft); Biological Physics (physics.bio-ph)
[15]  arXiv:1708.08568 (replaced) [pdf, other]
Title: How directional mobility affects biodiversity in rock-paper-scissors models