Physics - Biological Physics Publications (50)


Physics - Biological Physics Publications

A sperm-driven micromotor is presented as cargo-delivery system for the treatment of gynecological cancers. This particular hybrid micromotor is appealing to treat diseases in the female reproductive tract, the physiological environment that sperm cells are naturally adapted to swim in. Here, the single sperm cell serves as an active drug carrier and as driving force, taking advantage of its swimming capability, while a laser-printed microstructure coated with a nanometric layer of iron is used to guide and release the sperm in the desired area by an external magnet and structurally imposed mechanical actuation, respectively. Read More

The present work reports the formation and the characterization of antipleptic and symplectic metachronal waves in 3D cilia arrays immersed in a two-fluid environment, with a viscosity ratio of 20. A coupled lattice-Boltzmann-Immersed-Boundary solver is used. The periciliary layer is confined between the epithelial surface and the mucus. Read More

We present a nonlocal electrostatic formulation of nonuniform ions and water molecules with interstitial voids that uses a Fermi-like distribution to account for steric and correlation effects in electrolyte solutions. The formulation is based on the volume exclusion of hard spheres leading to a steric potential and Maxwell's displacement field with Yukawa-type interactions resulting in a nonlocal electric potential. The classical Poisson-Boltzmann model fails to describe steric and correlation effects important in a variety of chemical and biological systems, especially in high field or large concentration conditions found in and near binding sites, ion channels, and electrodes. Read More

We study the three-dimensional (3D) spatially-resolved distribution of the energy density of light in a 3D scattering medium upon the excitation of open transmission channels. The open transmission channels are excited by spatially shaping the incident optical wavefronts. To probe the local energy density, we excite isolated fluorescent nanospheres distributed inside the medium. Read More

The microtubule (MT) motor Kip3p is very processive kinesin that promotes catastrophes and pausing in particular on cortical contact. These properties explain the role of Kip3p in positioning the mitotic spindle in budding yeast and potentially other processes controlled by kinesin-8 family members. We present a theoretical approach to positioning of a MT network in a cell. Read More

Affiliations: 1Institute of Complex Systems and Institute for Advanced Simulation, Forschungszentrum Jülich, 2Department of Molecular Sensory Systems, Center of Advanced European Studies and Research, 3Department of Molecular Sensory Systems, Center of Advanced European Studies and Research, 4Department of Molecular Sensory Systems, Center of Advanced European Studies and Research, 5Institute of Complex Systems and Institute for Advanced Simulation, Forschungszentrum Jülich, 6Institute of Complex Systems and Institute for Advanced Simulation, Forschungszentrum Jülich

Sperm are propelled by bending waves travelling along the flagellum. During steering in gradients of sensory cues, sperm adjust the flagellar beat waveform. Symmetric and asymmetric beat waveforms produce straight and curved swimming paths, respectively. Read More

Understanding the thermally activated escape from a metastable state is at the heart of important phenomena such as the folding dynamics of proteins, the kinetics of chemical reactions or the stability of mechanical systems. In 1940 Kramers calculated escape rates both in the high damping and the low damping regime and suggested that the rate must have a maximum for intermediate damping. This phenomenon, today known as the Kramers turnover, has triggered important theoretical and numerical studies. Read More

The detection of gravity plays a fundamental role during the growth and evolution of plants. Although progress has been made in our understanding of the molecular, cellular and physical mechanisms involved in the gravity detection, a coherent scenario consistent with all the observations is still lacking. In this perspective paper we discuss recent experiments showing that the response to inclination of shoots is independent of the gravity intensity, meaning that the gravity sensor detects an inclination and not a force. Read More

We develope a two-species exclusion process with a distinct pair of entry and exit sites for each species of rigid rods. The relatively slower forward stepping of the rods in an extended bottleneck region, located in between the two entry sites, controls the extent of interference of the co-directional flow of the two species of rods. The relative positions of the sites of entry of the two species of rods with respect to the location of the bottleneck are motivated by a biological phenomenon. Read More

By means of a recently-proposed metric or structural derivative, called scale-q-derivative approach, we formulate differential equation that models the cell death by a radiation exposure in tumor treatments. The considered independent variable here is the absorbed radiation dose D instead of usual time. The survival factor, Fs, for radiation damaged cell obtained here is in agreement with the literature on the maximum entropy principle, as it was recently shown and also exhibits an excellent agreement with the experimental data. Read More

The nature of excited states of open quantum systems produced by incoherent natural thermal light is analyzed based on a description of the generator of the dynamics. Natural thermal light is shown to generate long-lasting coherent dynamics because of (i) the super-Ohmic character of the radiation, and (ii) the absence of pure dephasing dynamics. In the presence of an environment, the long-lasting coherences induced by suddenly turned-on incoherent light dissipate and stationary coherences are established. Read More

We study the existence and stability of stationary solutions of Poisson-Nernst- Planck equations with steric effects (PNP-steric equations) with two counter-charged species. These equations describe steady current through open ionic channels quite well. The current levels in open ionic channels are known to switch between `open' or `closed' states in a spontaneous stochastic process called gating, suggesting that their governing equations should give rise to multiple stationary solutions that enable such multi-stable behavior. Read More

Understanding the relationship between spontaneous stochastic fluctuations and the topology of the underlying gene regulatory network is fundamental for the study of gene expression, especially at the molecular level. Here by solving the analytical steady-state distribution of the protein copy number in a general kinetic model of gene expression, we reveal a quantitative relation between stochastic fluctuations and feedback regulation at the single-molecule level, which provides novel insights into how and to what extent a feedback loop can enhance or suppress molecular fluctuations. Based on such relation, we also develop an effective method to extract the topological information of gene regulatory networks from single-cell gene expression data. Read More

Many species of millimetric fungus-harvesting termites collectively build uninhabited, massive mound structures enclosing a network of broad tunnels which protrude from the ground meters above their subterranean nests. It is widely accepted that the purpose of these mounds is to give the colony a controlled micro-climate in which to raise fungus and brood by managing heat, humidity, and respiratory gas exchange. While different hypotheses such as steady and fluctuating external wind and internal metabolic heating have been proposed for ventilating the mound, the absence of direct in-situ measurement of internal air flows has precluded a definitive mechanism for this critical physiological function. Read More

Stick-slip, manifest as intermittent tangential motion between two solids, is a well-known friction instability that occurs in a number of natural and engineering systems. In the context of adhesive polymer interfaces, this phenomenon has often been solely associated with Schallamach waves, which are termed slow waves due to their low propagation speeds. We study the dynamics of a model polymer interface using coupled force measurements and high speed \emph{in situ} imaging, to explore the occurrence of stick-slip linked to other slow wave phenomena. Read More

Optical tweezers have enabled important insights into intracellular transport through the investigation of processive motor proteins, owing to the ability to manipulate particles at the nanoscale with force resolution in femto newtons. These studies typically utilize spherical cargoes as handles to probe the motor motion. The motor proteins operate under varying load forces, necessitating studies under controlled forces to understand their response to different loading conditions. Read More

Living cells use phase separation and concentration gradients to organize chemical compartments in space. Here, we present a theoretical study of droplet dynamics in gradient systems. We derive the corresponding growth law of droplets and find that droplets exhibit a drift velocity and position dependent growth. Read More

We study a model of seed dispersal that consists of an animal moving diffusively, feeding on fruits and dispersing the seeds, which are later deposited and capable of germination. The dynamics depends on several population parameters of growth, decay, harvesting, transport, digestion and germination. In particular, the deposition of transported seeds at places away from their collection sites produces a delay in the dynamics, whose effects are the focus of this work. Read More

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 distributed to maximize flux. Read More

The ability of the mammalian ear in processing high frequency sounds, up to $\sim$100 kHz, is based on the capability of outer hair cells (OHCs) responding to stimulation at high frequencies. These cells show a unique motility in their cell body coupled with charge movement. With this motile element, voltage changes generated by stimuli at their hair bundles drives the cell body and that, in turn, amplifies the stimuli. Read More

Uncovering the mechanisms that control size, growth, and division rates of systems reproducing through binary division means understanding basic principles of their life cycle. Recent work has focused on how division rates are regulated in bacteria and yeast, but this question has not yet been addressed in more complex, multicellular organisms. We have acquired a unique large-scale data set on the growth and asexual reproduction of two freshwater planarian species, Dugesia japonica and Dugesia tigrina, which reproduce by transverse fission and succeeding regeneration of head and tail pieces into new planarians. Read More

Action potentials (AP) are considered to be electrical phenomena. However, non-electrical changes at the cell surface have been reported and resulted in contradictions with the classical theory. The evidence presented herein corroborates that an AP is not a purely electrical phenomenon. Read More

Energetic ions lose their energy in tissue mainly by ionising its molecules. This produces secondary electrons which transport this energy radially away from the ion path. The ranges of most of these electrons do not exceed a few nanometres, therefore large energy densities (radial doses) are produced within a narrow region around the ion trajectory. Read More

We demonstrate the determination of the location of the distal-end of a fibre-optic device deep in tissue through the imaging of ballistic and snake photons using a time resolved single-photon detector array. The position was determined to centimetre accuracy, within clinically relevant settings and models. This technique can overcome the limitations imposed by tissue scattering in optically determining the in vivo location of fibre-optic medical instruments. Read More

Bacterial colonies are abundant on living and non-living surfaces and are known to mediate a broad range of processes in ecology, medicine and industry. Although extensively researched, from single cells to demographic scales, a comprehensive biomechanical picture, highlighting the cell-to-colony dynamics, is still lacking. Here, using molecular dynamics simulations and continuous modelling, we investigate the geometrical and mechanical properties of a bacterial colony growing on a substrate with free boundary, and demonstrate that such an expanding colony self-organizes into a "mosaic" of micro-domains consisting of highly aligned cells. Read More

We study stochastic dynamics of an inclusion within a one dimensional confined viscous active fluid. To highlight various features and to appeal to different contexts, the inclusion is in turn treated as a rigid element, an elastic element and a viscoelastic (Kelvin-Voigt) element. We show that the dynamics for the shape and position of the inclusion can be described by coupled Langevin equations with a confining potential and multiplicative noise. Read More

We investigate the effect of stress fluctuations on the stochastic dynamics of an inclusion embedded in a viscous gel. We show that, in non-equilibrium systems, stress fluctuations give rise to an effective attraction towards the boundaries of the confining domain, which is reminiscent of an active Casimir effect. We apply our result to the dynamics of deformations of the cell nucleus and we demonstrate the appearance of a fluctuation maximum at a critical level of activity, in agreement with recent experiments (Makhija et al. Read More

We discuss the gauge field theory approach to protein structure study, which allows a natural way to introduce collective degrees of freedom and nonlinear topological structures. Local symmetry of proteins and its breaking in the medium is considered, what allows to derive Abelian Higgs model of protein backbone, correct folding of which is defined by gauge symmetry breaking due hydrophobic forces. Within this model structure of protein backbone is defined by superposition of one-dimensional topological solitons (kinks), what allows to reproduce the three-dimensional structure of the protein backbone with precision up to 1A and to predict its dynamics. Read More

It is well known in enzyme kinetics that the Michaelis-Menten (MM) equation is applicable only to enzymes in the steady state. We show that the result obtained in the previous work [Phys. Rev. Read More

Biochemical feedback leads to dynamical transitions between cellular states, reminiscent of phase transitions in equilibrium systems. Yet cells are far from equilibrium. Here we show using a generic birth-death model that despite being far from equilibrium, biochemical feedback near a bifurcation point exhibits the scaling exponents of the mean-field universality class. Read More

Cross-linked filament bundles, such as in cilia and flagella, are ubiquitous in biology. They are considered in textbooks as simple filaments with larger stiffness. Recent observations of flagellar counterbend, however, show that induction of curvature in one section of a passive flagellum instigates a compensatory counter-curvature elsewhere, exposing the intricate role of the diminutive cross-linking proteins at large-scales. Read More

The mechanisms by which organs acquire their functional structure and realize its maintenance (or homeostasis) over time are still largely unknown. In this paper, we investigate this question on adipose tissue. Adipose tissue can represent 20 to 50% of the body weight. Read More

Inspired by recent experiments using synthetic microswimmers to manipulate droplets, we investigate the low-Reynolds-number locomotion of a model swimmer (a spherical squirmer) encapsulated inside a droplet of comparable size in another viscous fluid. Meditated solely by hydrodynamic interactions, the encaged swimmer is seen to be able to propel the droplet, and in some situations both remain in a stable co-swimming state. The problem is tackled using both an exact analytical theory and a numerical implementation based on boundary element method, with a particular focus on the kinematics of the co-moving swimmer and droplet in a concentric configuration, and we obtain excellent quantitative agreement between the two. Read More

Bacterial motility, and in particular repulsion or attraction towards specific chemicals, has been a subject of investigation for over 100 years, resulting in detailed understanding of bacterial chemotaxis and the corresponding sensory network in many bacterial species. For Escherichia coli most of the current understanding comes from the experiments with low levels of chemotactically-active ligands. However, chemotactically-inactive chemical species at concentrations found in the human gastrointestinal tract produce significant changes in E. Read More

We combine extensive data analyses with a modeling approach to measure, disentangle, and reconstruct the actual functional form of interactions involved in the coordination of swimming in Rummy-nose tetra (Hemigrammus rhodostomus). This species of fish performs burst-and-coast swimming behavior that consists of sudden heading changes combined with brief accelerations followed by quasi-passive, straight decelerations. We quantify the spontaneous stochastic behavior of a fish and the interactions that govern wall avoidance and the attraction and alignment to a neighboring fish, the latter by exploiting general symmetry constraints for the interactions. Read More

In this pedagogical paper a coherent explanation of the resting potential of nerve cells is given in terms of its determining factors. These are the currents of active transport of the ions to which the membrane is permeable, their membrane permeabilities and their concentrations in the extracellular fluid. They play the role of the independent variables in the problem and simultaneously also determine the concentrations of the permeating ions inside the cell. Read More

Native horse mucus is characterized with micro- and macrorheology and compared to hydroxyethylcellulose (HEC) gel as a model. Both systems show comparable viscoelastic properties on the microscale and for the HEC the macrorheology is in good agreement with the microrheology. For the mucus, the viscoelastic moduli on the macroscale are several orders of magnitude larger than on the microscale. Read More

Anticipated synchronization (AS) is a counter intuitive behavior that has been observed in several systems. When AS establishes in a sender-receiver configuration, the latter can predict the future dynamics of the former for certain parameter values. In particular, in neuroscience AS was proposed to explain the apparent discrepancy between information flow and time lag in the cortical activity recorded in monkeys. Read More

We investigate the role of greed on the lifetime of a random-walking forager on an initially resource-rich lattice. Whenever the forager lands on a food-containing site, all the food there is eaten and the forager can hop $\mathcal{S}$ more steps without food before starving. Upon reaching an empty site, the forager comes one time unit closer to starvation. Read More

In the immune system, T cells can quickly discriminate between foreign and self ligands with high accuracy. There is significant evidence T-cells achieve this remarkable performance utilizing a network architecture based on kinetic proofreading (KPR). KPR-based mechanisms actively consume energy to increase the specificity beyond what is possible in equilibrium. Read More

Individual computations and social interactions underlying collective behavior in groups of animals are of great ethological, behavioral, and theoretical interest. While complex individual behaviors have successfully been parsed into small dictionaries of stereotyped behavioral modes, studies of collective behavior largely ignored these findings; instead, their focus was on inferring single, mode-independent social interaction rules that reproduced macroscopic and often qualitative features of group behavior. Here we bring these two approaches together to predict individual swimming patterns of adult zebrafish in a group. Read More

We carried out dynamic force manipulations $in$ $silico$ on a variety of superhelical protein fragments from myosin, chemotaxis receptor, vimentin, fibrin, and phenylalanine zippers that vary in size and topology of their $\alpha$-helical packing. When stretched along the superhelical axis, all superhelices show elastic, plastic, and inelastic elongation regimes, and undergo a dynamic transition from the $\alpha$-helices to the $\beta$-sheets, which marks the onset of plastic deformation. Using Abeyaratne-Knowles formulation of phase transitions, we developed a theory to model mechanical and kinetic properties of protein superhelices under mechanical non-equilibrium conditions and to map their energy landscapes. Read More

The propagation of a beneficial mutation in a spatially extended population is usually studied using the phenomenological stochastic Fisher-Kolmogorov (SFKPP) equation. We derive here an individual based, stochastic model founded on the spatial Moran process where fluctuations are treated exactly. At high selection pressure, the results of this model are different from the classical FKPP. Read More

Stronger selection implies faster evolution---that is, the greater the force, the faster the change. This apparently self-evident proposition, however, is derived under the assumption that genetic variation within a population is primarily supplied by mutation (i.e. Read More

Purpose: To investigate the effect of realistic microstructural geometry on the susceptibility-weighted magnetic resonance (MR) signal in white matter (WM), with application to demyelination. Methods: Previous work has modeled susceptibility-weighted signals under the assumption that axons are cylindrical. In this work, we explore the implications of this assumption by considering the effect of more realistic geometries. Read More

We study pattern formation aspects in a 2-D reaction-diffusion (RD) sub-cellular model characterizing the effect of a spatial gradient of a plant hormone distribution on a family of G-proteins associated with root-hair (RH) initiation in the plant cell \emph{Arabidopsis thaliana}. The activation of these G-proteins, known as the Rho of Plants (ROPs), by the plant hormone auxin, is known to promote certain protuberances on root hair cells, which are crucial for both anchorage and the uptake of nutrients from the soil. Our mathematical model for the activation of ROPs by the auxin gradient is an extension of the model proposed by Payne and Grierson [PLoS ONE, {\bf 12}(4), (2009)], and consists of a two-component generalized Schnakenberg RD system with spatially heterogeneous coefficients on a 2-D domain. Read More

Affiliations: 1Arnold-Sommerfeld-Center for Theoretical Physics and Center for NanoScience, Department of Physics, Ludwig-Maximilians-Universität München, 2Arnold-Sommerfeld-Center for Theoretical Physics and Center for NanoScience, Department of Physics, Ludwig-Maximilians-Universität München

Transport of molecular motors along protein filaments in a half-closed geometry is a common feature of biologically relevant processes in cellular protrusions. Using a lattice gas model we study how the interplay between active and diffusive transport and mass conservation leads to localised domain walls and tip localisation of the motors. We identify a mechanism for task sharing between the active motors (maintaining a gradient) and the diffusive motion (transport to the tip), which ensures that energy consumption is low and motor exchange mostly happens at the tip. Read More

Many of the most important processes in cells take place on and across membranes. With the rise of an impressive array of powerful quantitative methods for characterizing these membranes, it is an opportune time to reflect on the structure and function of membranes from the point of view of biological numeracy. To that end, in this article, I review the quantitative parameters that characterize the mechanical, electrical and transport properties of membranes and carry out a number of corresponding order of magnitude estimates that help us understand the values of those parameters. Read More

Platonic solids such as polyhedra based on DNA have been deployed for multifarious applications such as RNAi delivery, biological targeting and bioimaging. All of these applications hinge on the capability of DNA polyhedra for molecular display with high spatial precision. Therefore high resolution structural models of such polyhedra are critical to widen their applications in both materials and biology. Read More

In a conformational nonequilibrium steady state (cNESS), enzyme turnover is modulated by the underlying conformational dynamics. Based on a discrete kinetic network model, we use the integrated population flux balance method to derive the cNESS turnover rate for a conformation-modulated enzymatic reaction. The traditional Michaelis-Menten (MM) rate equation is extended to a generalized form, which includes non-MM corrections induced by conformational population currents within combined cyclic kinetic loops. Read More