Physics - Biological Physics Publications (50)

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Physics - Biological Physics Publications

Myxobacteria are social bacteria, that can glide in 2D and form counter-propagating, interacting waves. Here we present a novel age-structured, continuous macroscopic model for the movement of myxobacteria. The derivation is based on microscopic interaction rules that can be formulated as a particle-based model and set within the SOH (Self-Organized Hydrodynamics) framework. Read More


An instability of a liquid droplet traversed by an energetic ion is explored. This instability is brought about by the predicted shock wave induced by the ion. An observation of multifragmentation of small droplets traversed by ions with high linear energy transfer is suggested to demonstrate the existence of shock waves. Read More


Advances in time resolved spectroscopy have provided new insight into the energy transmission in natural photosynthetic complexes. Novel theoretical tools and models are being developed in order to explain the experimental results. We provide a model calculation for the two-dimensional electronic spectra of Cholorobaculum tepidum which correctly describes the main features and transfer time scales found in recent experiments. Read More


We developed a new mechanical model for determining the compression and shear mechanical behavior of four different hemoglobin structures. Previous studies on hemoglobin structures have focused primarily on overall mechanical behavior; however, this study investigates the mechanical behavior of hemoglobin, a major constituent of red blood cells (RBCs), using steered molecular dynamics (SMD) simulations to obtain anisotropic mechanical behavior under compression and shear loading conditions. Four different configurations of hemoglobin molecules were considered: deoxyhemoglobin (deoxyHb), oxyhemoglobin (HbO2), carboxyhemoglobin (HbCO), and glycated hemoglobin (HbA1C). Read More


From a point of view of classical electrodynamics, the performance of two-dimensional shape-simplified antennae is discussed based upon the shape of naturally designed systems to harvest light. The modular design of nature is found to make the antenna non-reciprocal, hence more efficient. We further explain the reason that the light harvester must be a ring instead of a ball, the function of the notch at the LH1-RC complex, the non-heme iron at the reaction center, the chlorophylls are dielectric instead of conductor, a mechanism to prevent damages from excess sunlight, the functional role played by the long-lasting spectrometric signal observed, and the photon anti-bunching observed. Read More


Cells exhibit qualitatively different behaviors on substrates with different rigidities. The fact that cells are more polarized on the stiffer substrate motivates us to construct a two-dimensional cell with the distribution of focal adhesions dependent on substrate rigidities. This distribution affects the forces exerted by the cell and thereby determines its motion. Read More


Muon Spin Rotation is employed, for the first time, to investigate the spin dynamics of ferritin proteins isolated from the brain of an Alzheimer's disease (AD) patient and of a healthy control, using a reference sample of horse spleen ferritin. A model based on the N\'eel theory of superparamagnetism is developed in order to interpret the spin relaxation rate of the muons stopping in the core of the protein. In light of this model, our preliminary observations show that ferritins from the healthy control are filled with a mineral compatible with ferrihydrite, while ferritins from the AD patient contain a crystalline phase with a larger magnetocrystalline anisotropy, possibly magnetite or maghemite. Read More


Revealing the structure of complex biological macromolecules, such as proteins, is an essential step for understanding the chemical mechanisms that determine the diversity of their functions. Synchrotron based x-ray crystallography and cryo-electron microscopy have made major contributions in determining thousands of protein structures even from micro-sized crystals. They suffer from some limitations that have not been overcome, such as radiation damage, the natural inability to crystallize of a number of proteins and experimental conditions for structure determination that are incompatible with the physiological environment. Read More


Cytosine methylation has been found to play a crucial role in various biological processes, including a number of human diseases. The detection of this small modification remains challenging. In this work, we computationally explore the possibility of detecting methylated DNA strands through direct electrical conductance measurements. Read More


Precise localization of nanoparticles within a cell is crucial to the understanding of cell-particle interactions and has broad applications in nanomedicine. Here, we report a proof-of-principle experiment for imaging individual functionalized nanoparticles within a mammalian cell by correlative microscopy. Using a chemically-fixed, HeLa cell labeled with fluorescent core-shell nanoparticles as a model system, we implemented a graphene-oxide layer as a substrate to significantly reduce background scattering. Read More


Assuming a steady-state condition within a cell, metabolic fluxes satisfy an under-determined linear system of stoichiometric equations. Characterizing the space of fluxes that satisfy such equa- tions along with given bounds (and possibly additional relevant constraints) is considered of utmost importance for the understanding of cellular metabolism. Extreme values for each individual flux can be computed with Linear Programming (as Flux Balance Analysis), and their marginal distribu- tions can be approximately computed with Monte-Carlo sampling. Read More


We propose an extension of the cable equation by introducing a Caputo time fractional derivative. The fundamental solutions of the most common boundary problems are derived analitically via Laplace Transform, and result be written in terms of known special functions. This generalization could be useful to describe anomalous diffusion phenomena with leakage as signal conduction in spiny dendrites. Read More


The cable model is widely used in several fields of science to describe the propagation of signals. A relevant medical and biological example is the anomalous subdiffusion in spiny neuronal dendrites observed in several studies of the last decade. Anomalous subdiffusion can be modelled in several ways introducing some fractional component into the classical cable model. Read More


The small correction volume for conventional wavefront shaping methods limits their applications in biological imaging through scattering media. We demonstrate large volume wavefront shaping through a scattering layer with a single correction by conjugate adaptive optics and remote focusing (CAORF). The remote focusing module can keep the conjugation between the AO and scattering layer during three-dimensional scanning. Read More


Signal transduction within biological cells is governed by networks of interacting proteins. Communication between these proteins is mediated by signaling molecules which bind to receptors and induce stochastic transitions between different conformational states. Signaling is typically a cooperative process which requires the occurrence of multiple binding events so that reaction rates have a nonlinear dependence on the amount of signaling molecule. Read More


We review the status of protein-based molecular electronics. First we discuss fundamental concepts of electron transfer and transport in and across proteins and proposed mechanisms for these processes. We then describe the immobilization of proteins to solid-state surfaces in both nanoscale and macroscopic approaches, and highlight how different methodologies can alter protein electronic properties. Read More


An organism's ability to move freely is a fundamental behaviour in the animal kingdom. To understand animal locomotion requires a characterisation of the material properties, as well as the biomechanics and physiology. We present a biomechanical model of C. Read More


Ionic solutions are often regarded as fully dissociated ions dispersed in a polar solvent. While this picture holds for dilute solutions, at higher ionic concentrations, oppositely charged ions can associate into dimers, referred to as Bjerrum pairs. We consider the formation of such pairs within the nonlinear Poisson-Boltzmann framework, and investigate their effects on bulk and interfacial properties of electrolytes. Read More


We demonstrate the presence of chaos in stochastic simulations that are widely used to study biodiversity in nature. The investigation deals with a set of three distinct species that evolve according to the standard rules of mobility, reproduction and predation, with predation following the cyclic rules of the popular rock, paper and scissors game. The study uncovers the possibility to distinguish between time evolutions that start from slightly different initial states, guided by the Hamming distance which heuristically unveils the chaotic behavior. Read More


Magnetic resonance spectroscopy is universally regarded as one of the most important tools in chemical and bio-medical research. However, sensitivity limitations typically restrict imaging resolution to length scales greater than 10 \mu m. Here we bring quantum control to the detection of chemical systems to demonstrate high resolution electron spin imaging using the quantum properties of an array of nitrogen-vacancy (NV) centres in diamond. Read More


We present a theoretical analysis of the entanglement entropy of an open dimer, such as a photosynthetic biological system of two excited states of chlorophyll molecules interacting with a protein-solvent environment, modeled by a field of oscillators. We show that the entanglement entropy of the chlorophyll dimer is generated by its decoherence, caused by the environment interaction. Depending on the type of interaction, not all environment oscillators carry significant entanglement entropy. Read More


Chemotaxis, a basic and universal phenomenon among living organisms, directly controls the transport kinetics of active fluids such as swarming bacteria, but has not been considered when utilizing passive tracer to probe the nonequilibrium properties of such fluids. Here we present the first theoretical investigation of the diffusion dynamics of a chemoattractant-coated tracer in bacterial suspension, by developing a molecular dynamics model of bacterial chemotaxis. We demonstrate that the non-Gaussian statistics of full-coated tracer arises from the noises exerted by bacteria, which is athermal and exponentially correlated. Read More


Osteocytes and their cell processes reside in a large, interconnected network of voids pervading the mineralized bone matrix of most vertebrates. This osteocyte lacuno-canalicular network (OLCN) is believed to play important roles in mechanosensing, mineral homeostasis, and for the mechanical properties of bone. While the extracellular matrix structure of bone is extensively studied on ultrastructural and macroscopic scales, there is a lack of quantitative knowledge on how the cellular network is organized. Read More


The assembly of banana-shaped rodlike proteins on membranes, and the associated membrane shape transformations, are investigated by analytical theory and coarse-grained simulations. The membrane-mediated interactions between two banana-shaped inclusions are derived theoretically using a point-like formalism, both for zero surface tension and for finite surface tension. On a larger scale, the interactions between assemblies of such rodlike inclusions are determined analytically. Read More


We demonstrate near-atomic-resolution Bragg diffraction from aerosolized single granulovirus crystals using an x-ray free-electron laser. The form of the aerosol injector is nearly identical to conventional liquid-microjet nozzles, but the x-ray-scattering background is reduced by several orders of magnitude by the use of helium carrier gas rather than liquid. This approach provides a route to study the weak diffuse or lattice-transform signal arising from small crystals. Read More


A broad range of membrane proteins display anomalous diffusion on the cell surface. Different methods provide evidence for obstructed subdiffusion and diffusion on a fractal space, but the underlying structure inducing anomalous diffusion has never been visualized due to experimental challenges. We addressed this problem by imaging the cortical actin at high resolution while simultaneously tracking individual membrane proteins in live mammalian cells. Read More


Ensemble averaging experiments may conceal many fundamental molecular interactions. To overcome that, a high-throughput detection of single molecules or colloidal nanodots is crucial for biomedical, nanoelectronic, and solid-state applications. One-dimensional (1D) discrete flow of nanoscale objects is an efficient approach in this direction. Read More


We consider the chemotaxis problem for a one-dimensional system. To analyze the interaction of bacteria and attractant we use a modified Keller-Segel model which accounts attractant absorption. To describe the system we use the chemotaxis sensitivity function, which characterizes nonuniformity of bacteria distribution. Read More


We introduce a simple mechanical model for adherent cells that quantitatively relates cell shape, internal cell stresses and cell forces as generated by an anisotropic cytoskeleton. We perform experiments on the shape and traction forces of different types of cells with anisotropic morphologies, cultured on microfabricated elastomeric pillar arrays. We demonstrate that, irrespectively of the cell type, the shape of the cell edge between focal adhesions is accurately described by elliptical arcs, whose eccentricity expresses the ratio between directed and isotropic stresses. Read More


Fronts of compact bacterial colonies growing on a Petri dish are considered a paradigmatic instance of non-equilibrium fluctuations in the celebrated Eden, or Kardar-Parisi-Zhang (KPZ), universality class. However, while the experimental scaling exponent values crucially do not agree with Eden-based predictions, the source of this disagreement has remained poorly understood. We have performed growth experiments with E. Read More


We use stochastic rotation dynamics to examine the dynamics of the ejection of an initially strongly confined flexible polymer from a spherical capsid with and without hydrodynamics. The results obtained using SRD are compared to similar Langevin simulations. Inclusion of hydrodynamic modes speeds up the ejection but also allows the polymer to expand closer to equilibrium radius of gyration outside the capsid during ejection. Read More


Here we reveal details of the interaction between human lysozyme proteins, both native and fibrils, and their water environment by intense terahertz time domain spectroscopy. With the aid of a rigorous dielectric model, we determine the amplitude and phase of the oscillating dipole induced by the THz field in the volume containing the protein and its hydration water. At low concentrations, the amplitude of this induced dipolar response decreases with increasing concentration. Read More


This work introduces a novel reinterpretation of structured illumination (SI) microscopy for coherent imaging that allows three-dimensional imaging of complex refractive index (RI). To do so, we show that coherent SI is mathematically equivalent to a superposition of angled illuminations. It follows that raw acquisitions for standard SI-enhanced quantitative-phase images can be processed into complex electric-field maps describing sample diffraction under angled illuminations. Read More


An ancient repertoire of UV absorbing pigments which survive today in the phylogenetically oldest extant photosynthetic organisms the cyanobacteria point to a direction in evolutionary adaptation of the pigments and their associated biota from largely UVC absorbing pigments in the Archean to pigments covering ever more of the longer wavelength UV and visible in the Phanerozoic.Such a scenario implies selection of photon dissipation rather than photoprotection over the evolutionary history of life.This is consistent with the thermodynamic dissipation theory of the origin and evolution of life which suggests that the most important hallmark of biological evolution has been the covering of Earths surface with organic pigment molecules and water to absorb and dissipate ever more completely the prevailing surface solar spectrum. Read More


Sub-diffraction resolution imaging has played a pivotal role in biological research by visualizing key, but previously unresolvable, sub-cellular structures. Unfortunately, applications of far-field sub-diffraction resolution are currently divided between fluorescent and coherent-diffraction regimes, and a multimodal sub-diffraction technique that bridges this gap has not yet been demonstrated. Here we report that structured illumination (SI) allows multimodal sub-diffraction imaging of both coherent quantitative-phase (QP) and fluorescence. Read More


We present quantitative analysis on the competing effects of imposed shear and self-propulsion on the steady-state behavior of a dilute suspension of active, rodlike, Brownian particles (microswimmers) confined by the walls of a planar channel. To best capture the salient features of shear-induced effects, we consider the case of an imposed Couette flow, for which the shear rate is constant across the channel. We show that the steady-state behavior of microswimmers of different propulsion strengths, subject to flow of varying strength, can be explained in the light of a population splitting phenomenon. Read More


The functional window is an experimentally observed property of the avian compass that refers to its selectivity around the geomagnetic field strength. We show that the radical-pair model, using biologically feasible hyperfine parameters, can qualitatively explain the salient features of the avian compass as observed from behavioral experiments: its functional window, as well as disruption of the compass action by an RF field of specific frequencies. Further, we show that adjustment of the hyperfine parameters can tune the functional window, suggesting a possible mechanism for its observed adaptability to field variation. Read More


A key ecological parameter for planktonic copepods studies is their interspecies encounter rate which is driven by their behaviour and is strongly influenced by turbulence of the surrounding environment. A distinctive feature of copepods motility is their ability to perform quick displacements, often dubbed jumps, by means of powerful swimming strokes. Such a reaction has been associated to an escape behaviour from flow disturbances due to predators or other external dangers. Read More


We perform a static analysis of a circular cylinder laying at a liquid$-$gas interface and acting as a barrier between a surfactant-free surface and a surfactant-loaded surface. The respective surfaces have uniform surface tensions $\gamma_a$ and $\gamma_b$ that generate a surface tension imbalance $\Delta \gamma = \gamma_a - \gamma_b$. In addition to determining the general implications of the balances for forces and torques, we quantify how $\Delta \gamma$ influences the maximum load-bearing capacity of a floating cylinder for a specific set of parameters. Read More


In biophysics, the search for exact solutions of models of gene expression is more often than not a challenging task. Starting from the simplest problems, a small increase in complexity will often cause drastic complications, leaving us with few exact results. The mapping based on partitioning of Poisson arrivals (PPA-mapping) brings an alternative approach to the standard ones. Read More


Vertex models represent confluent tissue by polygonal or polyhedral tilings of space, with the individual cell interacting via force laws that depend on both the geometry of the cells and the topology of the tessellation. This dependence on the connectivity of the cellular network introduces several complications to performing molecular-dynamics-like simulations of vertex models, and in particular makes parallelizing the simulations difficult. cellGPU addresses this difficulty and lays the foundation for massively parallelized, GPU-based simulations of these models. Read More


The aim of this work is to propose a first coarse-grained model of Bacillus subtilis cell wall, handling explicitly the existence of multiple layers of peptidoglycans. In this first work, we aim at the validation of the recently proposed "three under two" principle. Read More


Experimental records of active bundle motility are used to demonstrate the presence of a low-dimensional chaotic attractor in hair cell dynamics. Dimensionality tests from dynamic systems theory are applied to estimate the number of independent variables sufficient for modeling the hair cell response. Poincare maps are constructed to observe a quasiperiodic transition from chaos to order with increasing amplitudes of mechanical forcing. Read More


Multidimensional systems coupled via complex networks are widespread in nature and thus frequently invoked for a large plethora of interesting applications. From ecology to physics, individual entities in mutual interactions are grouped in families, homogeneous in kind. These latter interact selectively, through a sequence of self-consistently regulated steps, whose deeply rooted architecture is stored in the assigned matrix of connections. Read More


We study the flocking and pattern formations of active particles with a Vicsek-like model that includes a configuration dependent noise term. In particular, we couple the strength of the noise with both the local density and orientation of neighboring particles. Our results show that such a configuration dependent noise can lead to the appearance of large-scale ordered and disordered patterns, without the need for any complex alignment interactions. Read More


The ordering of a multilayer consisting of DSPC bilayers on a silica sol substrate is studied within the model-independent approach to the reconstruction of profiles of the electron density from X-ray reflectometry data. It is found that the electroporation of bilayers in the field of anion silica nanoparticles significantly accelerates the process of their saturation with Na+ and H2O, which explains both a relatively small time of formation of the structure of the multilayer of 10^5 - 7x10^5 s and ~13 % excess of the electron density in it. Read More


Photosynthetic organisms rely on a series of self-assembled nanostructures with tuned electronic energy levels in order to transport energy from where it is collected by photon absorption, to reaction centers where the energy is used to drive chemical reactions. In the photosynthetic bacteria Chlorobaculum tepidum (Cba. tepidum), a member of the green sulphur bacteria (GSB) family, light is absorbed by large antenna complexes called chlorosomes. Read More


The 70 kDa Heat Shock Proteins Hsp70 have several essential functions in living systems, such as protecting proteins against protein aggregation, assisting protein folding, remodeling protein complexes and driving the translocation into organelles. These functions require high affinity for non-specific amino-acid sequences that are ubiquitous in proteins. It has been recently shown that this high affinity, called ultra-affinity, depends on a process driven out of equilibrium by ATP hydrolysis. Read More


Epithelial tissues form physically integrated barriers against the external environment protecting organs from infection and invasion. Within each tissue, epithelial cells respond to different challenges that can potentially compromise tissue integrity. In particular, cells collectively respond by reorganizing their cell-cell junctions and migrating directionally towards the sites of injury. Read More