Latest in physics.bio-ph

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Bees with attitude: the effect of gusts on flight dynamicsFeb 10 2018Flight is a complicated task at small scales in part due to the ubiquitous unsteady air which contains it. Flying organisms deal with these difficulties using active and passive control mechanisms to steer their body motion. Body attitudes of flapping ... More
Nonspecific biological effects of weak magnetic fields depend on molecular rotationsFeb 08 2018The radical pair mechanism is a leading hypothesis in animal magnetic navigation. This mechanism associates the magnetic sense with the visual system, the radical pairs in cryptochromes of the eye retina being specialized magnetic receptors that modulate ... More
Synergistic cumulative contagion in epidemic spreadingFeb 08 2018Most epidemic spreading models assume memoryless agents and independent transmissions along different infection channels. Nevertheless, many real-life cases are manifestly time-sensitive and show strong correlations. Although some recent research efforts ... More
Holographic Traction Force MicroscopyFeb 07 2018Traction Force Microscopy (TFM) computes the forces exerted at the surface of an elastic material by measuring induced deformations in volume. It is used to determine the pattern of the adhesion forces exerted by cells or by cellular assemblies grown ... More
Telling apart <I>Felidae</I> and <I>Ursidae</I> from the distribution of nucleotides in mitochondrial DNAFeb 07 2018Rank--frequency distributions of nucleotide sequences in mitochondrial DNA are defined in a way analogous to the linguistic approach, with the highest-frequent nucleobase serving as a whitespace. For such sequences, entropy and mean length are calculated. ... More
Towards Understanding the Structure, Dynamics and Bio-activity of Diabetic Drug MetforminFeb 07 2018Small molecules are often found to exhibit extraordinarily diverse biological activities. Metformin is one of them. It is widely used as anti-diabetic drug for type-two diabetes. In addition to that, metformin hydrochloride shows anti-tumour activities ... More
Exploiting ecology in drug pulse sequences in favour of population reductionFeb 07 2018A deterministic population dynamics model involving birth and death for a two-species system, comprising a wild-type and more resistant species competing via logistic growth, is subjected to two distinct stress environments designed to mimic those that ... More
On the role of multiple scales in metapopulations of public good producersFeb 07 2018Multiple scales in metapopulations can give rise to paradoxical behaviour: in a conceptual model for a public goods game, the species associated with a fitness cost due to the public good production can be stabilised in the well-mixed limit due to the ... More
Risk of coinfection outbreaks in temporal networks: a case study of a hospital contact networkFeb 07 2018We study the spreading of cooperative infections in an empirical temporal network of contacts between people, including health care workers and patients, in a hospital. The system exhibits a phase transition leading to one or several endemic branches, ... More
Role of atomic spin-mechanical coupling in the problem of magnetic biocompassFeb 07 2018It is a well established notion that animals can detect the Earth's magnetic field, while the biophysical origin of such magnetoreception is still elusive. Recently, a magnetic receptor Drosophila CG8198 (MagR) with a rod-like protein complex is reported ... More
Structure-stiffness relation of live mouse brain tissue determined by depth-controlled indentation mappingFeb 06 2018The mechanical properties of brain tissue play a pivotal role in neurodevelopment and neurological disorders. Yet, at present, there is no consensus on how the different structural parts of the tissue contribute to its stiffness variations. Here, we have ... More
Fidelity of bacterial translation initiation: a stochastic kinetic modelFeb 06 2018During the initiation stage of protein synthesis, a ribosomal initiation complex (IC) is assembled on a messenger RNA (mRNA) template. In bacteria, the speed and accuracy of this assembly process are regulated by the complementary activities of three ... More
Motility induces a double positive effect of E. coli dispersion in porous mediaFeb 06 2018The role of motility on the hydrodynamic dispersion of bacteria in a porous media is here studied by tracking thousands of bacteria in a microfluidic chip containing randomly placed obstacles. We first evaluate the dynamics of the spreading of two populations ... More
Automatic microtubule tracking in fluorescence images of cells doped with increasing concentrations of taxol and nocodazoleFeb 05 2018The purpose of this paper is to provide an algorithm for detecting and tracking astral MTs in a fully automated way and supply a description of their dynamic behaviour. For the algorithm testing, a dataset of stacks (i.e. time-lapse image sequences), ... More
Multilayer Network Modeling of Integrated Biological SystemsFeb 05 2018Biological systems, from a cell to the human brain, are inherently complex. A powerful representation of such systems, described by an intricate web of relationships across multiple scales, is provided by complex networks. Recently, several studies are ... More
Computation of a Theoretical Membrane Phase Diagram, and the Role of Phase in Lipid Raft-Mediated Protein OrganizationFeb 04 2018Lipid phase heterogeneity in the plasma membrane is thought to be crucial for many aspects of cell signaling, but the physical basis of participating membrane domains such as "lipid rafts" remains controversial. Here we consider a lattice model yielding ... More
Spatially-resolved Brillouin spectroscopy reveals biomechanical changes in early ectatic corneal disease and post-crosslinking in vivoFeb 04 2018Mounting evidence connects the biomechanical properties of tissues to the development of eye diseases such as keratoconus, a common disease in which the cornea thins and bulges into a conical shape. However, measuring biomechanical changes in vivo with ... More
Lipid-protein interaction induced domains: kinetics and conformational changes in multicomponent vesiclesFeb 03 2018The spatio-temporal organization of proteins and the associated morphological changes in membranes are of importance in cell signaling. Several mechanisms that promote the aggregation of proteins at low cell surface concentrations have been investigated ... More
How light absorption modifies the radiative force on a microparticle in optical tweezersFeb 02 2018Reflection and refraction of light can be used to trap small dielectric particles in the geometrical optics regime. Absorption of light is usually neglected in theoretical calculations, but it is known that it occurs in the optical trapping of metallic ... More
Excess-tuberculosis-mortality in young women: high accuracy explorationFeb 01 2018In a general way at all ages and for almost all diseases, male death rates are higher than female death rates. Here we report a case in which the opposite holds, namely for tuberculosis (TB) mortality between the ages of 5 and 25, female death rates are ... More
Complex Network Geometry and Frustrated SynchronizationFeb 01 2018The dynamics of networks of neuronal cultures has been recently shown to be strongly dependent on the network geometry and in particular on their dimensionality. However, this phenomenon has been so far mostly unexplored from the theoretical point of ... More
Langevin equations for the run-and-tumble of swimming bacteriaFeb 01 2018The run and tumble motions of a swimming bacterium are well characterized by two stochastic variables: the speed $v(t)$ and the change of direction or deflection \mbox{$x(t)=\cos\varphi(t)$}, where $\varphi(t)$ is the turning angle at time $t$. Recently, ... More
The free energy of biomembrane and nerve excitation and the role of anestheticsJan 31 2018In the electromechanical theory of nerve stimulation, the nerve impulse consists of a traveling region of solid membrane in a liquid environment. Therefore, the free energy necessary to stimulate a pulse is directly related to the free energy difference ... More
Landau-Ginzburg theory of cortex dynamics: Scale-free avalanches emerge at the edge of synchronizationJan 31 2018Understanding the origin, nature, and functional significance of complex patterns of neural activity, as recorded by diverse electrophysiological and neuroimaging techniques, is a central challenge in neuroscience. Such patterns include collective oscillations ... More
High-throughput intensity diffraction tomography with a computational microscopeJan 29 2018We demonstrate a motion-free intensity diffraction tomography technique that enables direct inversion of 3D phase and absorption from intensity-only measurements for weakly scattering samples. We derive a novel linear forward model, featuring slice-wise ... More
Age-dependent responses of organs to tuberculosis and cancerJan 29 2018Both tuberculosis (TB) and cancer (C) can affect many organs, e.g. brain, bones, skin. We consider the age-specific response of each organ j, particularly how fast lesions develop and how serious they become. A convenient identification of the response ... More
Brain-to-brain heteroclinic coordination: model of sequential episodic memory initiationJan 29 2018Retrieval of episodic memory is a dynamical process in the large scale brain networks. In social groups, the neural patterns, associated to specific events directly experienced by single members, are encoded, recalled and shared by all participants. Here ... More
Antimargination of microparticles and platelets in the vicinity of branching vesselsJan 26 2018We investigate the margination of microparticles/platelets in blood flow through complex geometries typical for in vivo vessel networks: a vessel confluence and a bifurcation. Using 3D Lattice-Boltzmann simulations, we find that behind the confluence ... More
Translocation Mobilities of Proteins in Nanopores: A Coarse-Grained Molecular Dynamics StudyJan 26 2018We investigate the translocation of a protein through model nanopores using coarse-grained (CG) non-equilibrium molecular dynamics (NEMD) simulations and compare the results with a continuum model. We considered the effects of nanopore confinement and ... More
Laser induced topological cues shape, guide, and anchor human Mesenchymal Stem CellsJan 25 2018This report focuses on the effect of the surface topography of the substrate on the behavior of human mesenchymal stem cells from bone marrow (MSCs) before and after co-differentiation into adipocytes and osteoblasts. Picosecond pulsed laser ablation ... More
Floating Forests: Quantitative Validation of Citizen Science Data Generated From Consensus ClassificationsJan 25 2018Large-scale research endeavors can be hindered by logistical constraints limiting the amount of available data. For example, global ecological questions require a global dataset, and traditional sampling protocols are often too inefficient for a small ... More
Convenient Interface to Inverse Ising (ConIII): A Python package for solving maximum entropy modelsJan 24 2018ConIII (pronounced CON-ee) is an open-source Python project providing a simple interface to solving maximum entropy models, with a focus on the Ising model. We describe the maximum entropy problem and give an overview of the algorithms that are implemented ... More
A Data-Driven Approach to Connection ModelingJan 24 2018The study of motion in animals and robots has been aided by insights from geometric mechanics. In friction dominated systems, a mechanical "connection" can provide a high fidelity mechanical model. The connection is a co-vector (Lie algebra) valued map ... More
Cell adhesion and fluid flow jointly initiate genotype spatial distribution in biofilmsJan 24 2018Biofilms are microbial collectives that occupy a diverse array of surfaces. The function and evolution of biofilms are strongly influenced by the spatial arrangement of different strains and species within them, but how spatiotemporal distributions of ... More
Perturbation approach for computing frequency- and time-resolved photon correlation functionsJan 24 2018We propose an alternative formulation of the sensor method presented in [Phys. Rev. Lett 109, 183601 (2012)] for the calculation of frequency-filtered and time-resolved photon correlations. Our approach is based on an algebraic expansion of the joint ... More
In vivo high resolution human retinal imaging with wavefront correctionless full-field OCTJan 24 2018As the lateral resolution of FFOCT with spatially incoherent illumination has been shown to be insensitive to aberrations, we demonstrate high resolution en face full-field OCT (FFOCT) retinal imaging without wavefront correction in the human eye in vivo ... More
Role of Internal Motions and Molecular Geometry on the NMR Relaxation of HydrocarbonsJan 23 2018The role of internal motions and molecular geometry on $^1$H NMR relaxation times $T_{1,2}$ in hydrocarbons is investigated using MD (molecular dynamics) simulations of the autocorrelation functions for in{\it tra}molecular $G_R(t)$ and in{\it ter}molecular ... More
Non-linear optical spectroscopy and two-photon excited fluorescence spectroscopy reveal the excited states of fluorophores embedded in beetle's elytraJan 23 2018Upon illumination by ultraviolet light, many animal species emit light through fluorescence processes arising from fluorophores embedded within their biological tissues. Fluorescence studies in living organisms are however relatively scarce and so far ... More
Transport of secondary electrons through coatings of ion-irradiated metallic nanoparticlesJan 21 2018Feb 05 2018The transport of low-energy electrons through the coating of a radiosensitizing metallic nanoparticle under fast ion irradiation is analyzed theoretically and numerically. As a case study, we consider a poly(ethylene glycol)-coated gold nanoparticle of ... More
Solvophobic and solvophilic contributions in the water-to-aqueous guanidinium chloride transfer free energy of model peptidesJan 15 2018We study the solvation free energy of two different conformations (helix and extended) of two different peptides (deca-alanine and deca-glycine) in two different solvents (water and aqueous guanidinium chloride, GdmCl). The free energies are obtained ... More
Measuring the Complexity of ConsciousnessJan 11 2018The quest for a scientific description of consciousness has given rise to new theoretical and empirical paradigms for the investigation of phenomenological contents as well as clinical disorders of consciousness. An outstanding challenge in the field ... More
Super-resolution fluorescence microscopy by stepwise optical saturationJan 10 2018Super-resolution fluorescence microscopy is an important tool in biomedical research for its ability to discern features smaller than the diffraction limit. However, due to its difficult implementation and high cost, the universal application of super-resolution ... More
Scale-free networks are rareJan 09 2018A central claim in modern network science is that real-world networks are typically "scale free," meaning that the fraction of nodes with degree $k$ follows a power law, decaying like $k^{-\alpha}$, often with $2 < \alpha < 3$. However, empirical evidence ... More
Recent Advances in Computational Modeling of ThrombosisJan 06 2018The study of thrombosis is crucial to understand and develop new therapies for diseases like deep vein thrombosis, diabetes related strokes, pulmonary embolism etc. The last two decades have seen an exponential growth in studies related to the blood clot ... More
Deformation of a biconcave-discoid capsule in extensional flow and electric fieldJan 06 2018Biconcave-discoid (empirical shape of a red blood cell) capsule finds numerous applications in the field of bio-fluid dynamics and rheology, apart from understanding the behavior of red blood cells (RBC) in blood flow. A detailed analysis is, therefore, ... More
Impulse-Response Approach to Elastobaric Model for ProteinsJan 05 2018A novel energy landscape model, ELM, for proteins recently explained a collection of incoherent, elastic neutron scattering data from proteins. The ELM of proteins considers the elastic response of the proton and its environment to the energy and momentum ... More
Protein Pattern FormationJan 04 2018Protein pattern formation is essential for the spatial organization of many intracellular processes like cell division, flagellum positioning, and chemotaxis. A prominent example of intracellular patterns are the oscillatory pole-to-pole oscillations ... More
MSM/RD: Coupling Markov state models of molecular kinetics with reaction-diffusion simulationsDec 21 2017Molecular dynamics (MD) simulations can model the interactions between macromolecules with high spatiotemporal resolution but at a high computational cost. By combining high-throughput MD with Markov state models (MSMs), it is now possible to obtain statistically ... More
Wide-Field Multiphoton Imaging Through Scattering MediaDec 20 2017We demonstrate an approach for wide-field multiphoton imaging through scattering media without any a priori knowledge or requirement to determine its properties. Temporal focusing is used to project light patterns in a Hadamard basis through a turbid ... More
Design principles for selective self-assembly of active networksDec 07 2017Living cells dynamically modulate the local morphologies of their actin cytoskeletons to perform biological functions, including force transduction, intracellular transport, and cell division. A major challenge is to understand how diverse structures ... More
Evolutionary dynamics of cooperation in neutral populationsDec 06 2017Cooperation is a difficult proposition in the face of Darwinian selection. Those that defect have an evolutionary advantage over cooperators who should therefore die out. However, spatial structure enables cooperators to survive through the formation ... More
Label-free optical vibrational spectroscopy to detect the metabolic state of M. tuberculosis cells at the site of diseaseDec 05 2017Tuberculosis relapse is a barrier to shorter treatment. It is thought that lipid rich cells, phenotypically resistant to antibiotics, may play a major role. Most studies investigating relapse use sputum samples although tissue bacteria may play an important ... More
The 2015 super-resolution microscopy roadmapNov 14 2017Far-field optical microscopy using focused light is an important tool in a number of scientific disciplines including chemical, (bio)physical and biomedical research, particularly with respect to the study of living cells and organisms. Unfortunately, ... More
Small animal whole body imaging with metamaterial-inspired RF coilNov 10 2017Preclinical magnetic resonance imaging often requires the entire body of an animal to be imaged with sufficient quality. This is usually performed by combining regions scanned with small coils with high sensitivity or long scans using large coils with ... More
A nucleobase-centered coarse-grained representation for structure prediction of RNA motifsNov 02 2017Dec 06 2017We introduce the SPlit-and-conQueR (SPQR) model, a coarse-grained representation of RNA designed for structure prediction and refinement. In our approach, the representation of a nucleotide consists of a point particle for the phosphate group and an anisotropic ... More
Two-photon photoactivated voltage imaging in tissue with an Archaerhodopsin-derived reporterOct 27 2017Robust voltage imaging in tissue remains a technical challenge. Existing combinations of genetically encoded voltage indicators (GEVIs) and microscopy techniques cannot simultaneously achieve sufficiently high voltage sensitivity, background rejection, ... More
Studying Light-Harvesting Models with Superconducting CircuitsOct 20 2017The process of photosynthesis, the main source of energy in the animate world, converts sunlight into chemical energy. The surprisingly high efficiency of this process is believed to be enabled by an intricate interplay between the quantum nature of molecular ... More
Individuals, Institutions, and Innovation in the Debates of the French RevolutionOct 18 2017The French Revolution brought principles of "liberty, equality, and brotherhood" to bear on the day-to-day challenges of governing what was then the largest country in Europe. Its experiments provided a model for future revolutions and democracies across ... More
Coupling Brain-Tumor Biophysical Models and Diffeomorphic Image RegistrationOct 16 2017We present the SIBIA (Scalable Integrated Biophysics-based Image Analysis) framework for joint image registration and biophysical inversion and we apply it to analyse MR images of glioblastomas (primary brain tumors). In particular, we consider the following ... More
Second-order freeriding on antisocial punishment restores the effectiveness of prosocial punishmentOct 12 2017Economic experiments have shown that punishment can increase public goods game contributions over time. However, the effectiveness of punishment is challenged by second-order freeriding and antisocial punishment. The latter implies that non-cooperators ... More
Analysis of biochemical mechanisms provoking differential spatial expression in Hh target genesSep 28 2017This work analyses the transcriptional effects of some biochemical mechanisms proposed in previous literature which attempts to explain the differential spatial expression of Hedgehog target genes involved in Drosophila development. Specifically, the ... More
Effects and limitations of a nucleobase-driven backmapping procedure for nucleic acids using steered Molecular DynamicsSep 25 2017Dec 14 2017Coarse-grained models can be of great help to address the problem of structure prediction in nucleic acids. On one hand they can make the prediction more efficient, while on the other hand, they can also help to identify the essential degrees of freedom ... More
Towards non-invasive cancer diagnostics and treatment based on electromagnetic fields, optomechanics and microtubulesAug 24 2017In this paper, we discuss biological effects of electromagnetic (EM) fields in the context of cancer biology. In particular, we review the nanomechanical properties of microtubules (MTs), the latter being one of the most successful targets for cancer ... More
Are there optical communication channels in the brain?Aug 23 2017Despite great progress in neuroscience, there are still fundamental unanswered questions about the brain, including the origin of subjective experience and consciousness. Some answers might rely on new physical mechanisms. Given that biophotons have been ... More
Why we live in hierarchies: a quantitative treatiseJul 06 2017This book is concerned with the various aspects of hierarchical collective behaviour which is manifested by most complex systems in nature. From the many of the possible topics, we plan to present a selection of those that we think are useful from the ... More
Topology determines force distributions in one-dimensional random spring networksJul 05 2017Jul 07 2017Networks of elastic fibers are ubiquitous in biological systems and often provide mechanical stability to cells and tissues. Fiber reinforced materials are also common in technology. An important characteristic of such materials is their resistance to ... More
Topology counts: force distributions in circular spring networksJul 05 2017Jul 07 2017Filamentous polymer networks govern the mechanical properties of many biological materials. Force distributions within these networks are typically highly inhomogeneous and, although the importance of force distributions for structural properties is well ... More
Correlations in magnitude series to assess nonlinearities: application to multifractal models and heartbeat fluctuationsMay 31 2017Sep 04 2017The correlation properties of the magnitudes of a time series (sometimes called volatility) are associated with nonlinear and multifractal properties and have been applied in a great variety of fields. Here, we have obtained analytically the expression ... More
Energy demands of diverse spiking cells from the neocortex, hippocampus, and thalamusMay 29 2017It has long been known that neurons in the brain are not physiologically homogeneous. In response to current stimulus, they can fire several distinct patterns of action potentials that are associated with different physiological classes ranging from regular-spiking ... More
Multiple scales and phases in discrete chains with application to folded proteinsMay 26 2017Chiral heteropolymers such as larger globular proteins can simultaneously support multiple length scales. The interplay between different scales brings about conformational diversity, and governs the structure of the energy landscape. Multiple scales ... More
Alliance formation with exclusion in the spatial public goods gameMay 24 2017Detecting defection and alarming partners about the possible danger could be essential to avoid being exploited. This act, however, may require a huge individual effort from those who take this job, hence such a strategy seems to be unfavorable. But structured ... More
Statistical physics of human cooperationMay 19 2017Extensive cooperation among unrelated individuals is unique to humans, who often sacrifice personal benefits for the common good and work together to achieve what they are unable to execute alone. The evolutionary success of our species is indeed due, ... More
Comparison of Decision Tree Based Classification Strategies to Detect External Chemical Stimuli from Raw and Filtered Plant Electrical ResponseMay 13 2017Plants monitor their surrounding environment and control their physiological functions by producing an electrical response. We recorded electrical signals from different plants by exposing them to Sodium Chloride (NaCl), Ozone (O3) and Sulfuric Acid (H2SO4) ... More
Absence of selection for quantum coherence in the Fenna-Matthews-Olson complex: a combined evolutionary and excitonic studyMay 02 2017We present a study on the evolution of the Fenna-Matthews-Olson bacterial photosynthetic pigment-protein complex. This protein complex functions as an antenna. It transports absorbed photons - excitons - to a reaction center where photosynthetic reactions ... More
Effect of Surfaces on Amyloid Fibril FormationApr 26 2017Using atomic force microscopy (AFM) we investigated the interaction of amyloid beta (Ab) (1 42) peptide with chemically modified surfaces in order to better understand the mechanism of amyloid toxicity, which involves interaction of amyloid with cell ... More
Cu2+ Affects Amyloid-\b{eta} (1-42) Aggregation by Increasing Peptide-Peptide Binding ForcesApr 26 2017The link between metals, Alzheimers disease (AD) and its implicated protein, amyloid \b{eta} (A\b{eta}), is complex and highly studied. AD is believed to occur as a result of the misfolding and aggregation of A\b{eta}. The dyshomeostasis of metal ions ... More
Magnetic Force Microscopy Characterization of Superparamagnetic Iron Oxide Nanoparticles (SPIONs)Apr 26 2017Superparamagnetic iron oxide nanoparticles (SPIONs), due to their controllable sizes, relatively long in vivo half-life and limited agglomeration, are ideal for biomedical applications such as magnetic labeling, hyperthermia cancer treatment, targeted ... More
Label-free three-dimensional (3D) structural imaging in live cells using intrinsic optical refractive indexApr 14 2017Here we report a method for visualization of volumetric structural information of live biological samples with no exogenous contrast agents. The process is made possible through a technique that involves generation, synthesis and analysis of three-dimensional ... More
Quantifying protein densities on cell membranes using super-resolution optical fluctuation imagingApr 05 2017Surface molecules, distributed in diverse patterns and clusters on cell membranes, influence vital functions of living cells. It is therefore important to understand their molecular surface organisation under different physiological and pathological conditions. ... More
Experimental measurement of binding energy, selectivity and allostery using fluctuation theoremsMar 30 2017Thermodynamic bulk measurements of binding reactions critically rely on the validity of the law of mass action and the assumption of a dilute solution. Yet important biological systems such as allosteric ligand-receptor binding, macromolecular crowding, ... More
Statistical mechanics for metabolic networks during steady-state growthMar 06 2017Which properties of metabolic networks can be derived solely from stoichiometric information about the network's constituent reactions? Predictive results have been obtained by Flux Balance Analysis (FBA), by postulating that cells set metabolic fluxes ... More
Absolute bacterial cell enumeration using flow cytometryMar 02 2017Jun 20 2017Aim: To evaluate a flow cytometry protocol that uses reference beads for the enumeration of live and dead bacteria present in a mixture. Methods and Results: Mixtures of live and dead Escherichia coli with live:dead concentration ratios varying from 0 ... More
Role-separating ordering in social dilemmas controlled by topological frustrationFeb 27 2017"Three is a crowd" is an old proverb that applies as much to social interactions, as it does to frustrated configurations in statistical physics models. Accordingly, social relations within a triangle deserve special attention. With this motivation, we ... More
Human brain ferritin studied by muon Spin Rotation: a pilot studyFeb 21 2017May 22 2017Muon Spin Rotation is employed 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 sample of horse-spleen ferritin as a reference. A model based on the ... More
An analytic approximation of the feasible space of metabolic networksFeb 17 2017Apr 06 2017Assuming 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 equations along with given bounds (and possibly additional relevant ... More
Quantum magnetic resonance microscopyFeb 14 2017Magnetic 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 ... More
Spatial dynamics of synthetic microbial hypercycles and their parasitesJan 17 2017Early theoretical work revealed that the simplest class of autocatalytic cycles, known as hypercycles, provide an elegant framework for understanding the evolution of mutualism. Furthermore, hypercycles are highly susceptible to parasites, spatial structure ... More
Tensor clustering with algebraic constraints gives interpretable groups of crosstalk mechanisms in breast cancerDec 24 2016Apr 28 2017We introduce a tensor-based clustering method to extract sparse, low-dimensional structure from high-dimensional, multi-indexed datasets. Specifically, this framework is designed to enable detection of clusters of data in the presence of structural requirements ... More
Embedding of biological distribution networks with differing environmental constraintsDec 23 2016Distribution networks -- from vasculature to urban transportation systems -- are prevalent in both the natural and consumer worlds. These systems are intrinsically physical in composition and are embedded into real space, properties that lead to constraints ... More
Ionic Coulomb blockade and anomalous mole fraction effect in NaChBac bacterial ion channelsDec 08 2016We report an experimental study of the influences of the fixed charge and bulk ionic concentrations on the conduction of biological ion channels, and we consider the results within the framework of the ionic Coulomb blockade model of permeation and selectivity. ... More
A Thermodynamically consistent model of the post-translational Kai circadian clockDec 08 2016The principal pacemaker of the circadian clock of the cyanobacterium S. elongatus is a protein phosphorylation cycle consisting of three proteins, KaiA, KaiB and KaiC. KaiC forms a homohexamer, with each monomer consisting of two domains, CI and CII. ... More
Subsampled Phase Retrieval for On-chip Lensless Holographic VideoDec 07 2016On-chip holographic video is a convenient way to monitor biological samples simultaneously at high spatial resolution and over a wide field-of-view. However, due to the limited readout rate of digital detector arrays, one often faces a tradeoff between ... More
Quantifying brain microstructure with diffusion MRI: Theory and parameter estimationDec 06 2016We review, systematize and discuss models of diffusion in neuronal tissue, by putting them into an overarching physical context of coarse-graining over an increasing diffusion length scale. From this perspective, we view research on quantifying brain ... More
Structural characterization and statistical-mechanical model of epidermal patternsDec 06 2016In proliferating epithelia of mammalian skin, cells of irregular polygonal-like shapes pack into complex nearly flat two-dimensional structures that are pliable to deformations. In this work, we employ various sensitive correlation functions to quantitatively ... More
Assisted conduction in molecular wire and related quantum biological processesDec 06 2016We present a detailed study of the conduction properties of a molecular wire where hopping process between electronic sites is coupled to a molecular vibrational mode. The molecule is sandwiched between two electronic leads at finite temperatures. We ... More
Biological signaling by interfacial sound pulses. A physics approachDec 06 2016Biological signaling is imagined as a combination of activation and transport. The former is triggered by local molecular interactions and the latter is the result of molecular diffusion. However, other fundamental physical principles of communication ... More
Symplectic and antiplectic waves in an array of beating cilia attached to a curved bodyDec 06 2016By taking into account the hydrodynamic interactions in a one dimensional array of model cilia, attached to a curved no-slip surface, we investigate their synchronized motion. We show, how does the emergence of metachronal waves depend on the initial ... More
High-resolution Collinear Chiral Sum Frequency Generation Microscopy by Using Vectorial BeamDec 06 2016In chiral sum frequency generation (C-SFG), the chiral nature of ${\chi}^{(2)}$ requires the three involved electric fields to be pairwise non-parallel, leading to the traditional non-collinear configuration which is a hindrance for achieving diffraction ... More
Zipf's law, unbounded complexity and open-ended evolutionDec 06 2016A major problem for evolutionary theory is understanding the so called {\em open-ended} nature of evolutionary change. Open-ended evolution (OEE) refers to the unbounded increase in complexity that seems to characterise evolution on multiple scales. This ... More
Towards multistage modelling of protein dynamics with monomeric Myc oncoprotein as an exampleDec 05 2016We propose to combine a mean field approach with all atom molecular dynamics into a multistage algorithm that can model protein folding and dynamics over very long time periods yet with atomic level precision. As an example we investigate an isolated ... More