Latest in q-bio.sc

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How kinesin waits for ATP affects the nucleotide and load dependence of the stepping kineticsAug 20 2019Dimeric molecular motors walk on polar tracks by binding and hydrolyzing one ATP per step. Despite tremendous progress, the waiting state for ATP binding in the well-studied kinesin that walks on microtubule (MT), remains controversial. One experiment ... More
Epiphoresis: a nonequilibrium mechanism for fast search on DNAAug 19 2019Vital biological processes such as genome repair require fast and efficient binding of selected proteins to specific target sites on DNA. Here we propose an active target search mechanism based on "epiphoresis", the dynamics of DNA-binding proteins up ... More
Organization of fast and slow chromatin revealed by single-nucleosome dynamicsAug 16 2019Understanding chromatin organization and dynamics is important since they crucially affect DNA functions. In this study, we investigate chromatin dynamics by statistically analyzing single-nucleosome movement in living human cells. Bi-modal nature of ... More
Stability Analysis of a Bulk-Surface Reaction Model for Membrane-Protein ClusteringAug 14 2019Protein aggregation on the plasma membrane (PM) is of critical importance to many cellular processes such as cell adhesion, endocytosis, fibrillar conformation, and vesicle transport. Lateral diffusion of protein aggregates or clusters on the surface ... More
Physical limit to concentration sensing in a changing environmentAug 12 2019Cells adapt to changing environments by sensing ligand concentrations using specific receptors. The accuracy of sensing is ultimately limited by the finite number of ligand molecules bound by receptors. Previously derived physical limits to sensing accuracy ... More
Target search on DNA by interacting molecules: First-passage approachAug 09 2019Gene regulation is one of the most important fundamental biological processes in living cells. It involves multiple protein molecules that locate specific sites on DNA and assemble gene initiation or gene repression multi-molecular complexes. While the ... More
On the Role of Vesicle Transport in Neurite Growth: Modelling and ExperimentsAug 06 2019The processes that determine the establishment of the complex morphology of neurons during development are still poorly understood. We present experiments that use live imaging to examine the role of vesicle transport and propose a lattice-based model ... More
Molecular Brightness analysis of GPCR oligomerization in the presence of spatial heterogeneityJul 25 2019Measuring the oligomerization of plasma membrane proteins is rife with biophysical and biomedical implications. This is particularly true for GPCRs, a large family of proteins representing the targets of over one third of all FDA approved medications. ... More
Cell-to-cell variability in organelle abundance reveals mechanisms of organelle biogenesisJul 24 2019How cells regulate the number of organelles is a fundamental question in cell biology. While decades of experimental work have uncovered four fundamental processes that regulate organelle biogenesis, namely, de novo synthesis, fission, fusion and decay, ... More
An equilibrium model for ribosome competitionJul 22 2019The amount of ribosomes in a cell is considered as limiting, and gene expression is thus largely determined by their cellular concentration. In this work we develop a toy-model to study the trade-off between the ribosomal supply and the demand of the ... More
A probabilistic approach to extreme statistics of Brownian escape times in dimensions 1, 2, and 3Jul 17 2019First passage time (FPT) theory is often used to estimate timescales in cellular and molecular biology. While the overwhelming majority of studies have focused on the time it takes a given single Brownian searcher to reach a target, cellular processes ... More
Cytoskeletal filament length controlled dynamic sequestering of intracellular cargoJul 15 2019The spatial localization or sequestering of motile cargo and their dispersal within cells is an important process in a number of physiological contexts. The morphology of the cytoskeletal network, along which active, motor-driven intracellular transport ... More
Lattice models for protein organization throughout thylakoid membrane stacksJul 11 2019Proteins in photosynthetic membranes can organize into patterned arrays that span the membrane's lateral size. Attractions between proteins in different layers of a membrane stack can play a key role in this ordering, as was suggested by microscopy and ... More
Optimizing defence, counter-defence and counter-counter defence in parasitic and trophic interactions -- A modelling studyJul 10 2019In host-pathogen interactions, often the host (attacked organism) defends itself by some toxic compound and the parasite, in turn, responds by producing an enzyme that inactivates that compound. In some cases, the host can respond by producing an inhibitor ... More
Quantitative Immunology for PhysicistsJul 08 2019The adaptive immune system is a dynamical, self-organized multiscale system that protects vertebrates from both pathogens and internal irregularities, such as tumours. For these reason it fascinates physicists, yet the multitude of different cells, molecules ... More
Quantitative Immunology for PhysicistsJul 08 2019Jul 28 2019The adaptive immune system is a dynamical, self-organized multiscale system that protects vertebrates from both pathogens and internal irregularities, such as tumours. For these reason it fascinates physicists, yet the multitude of different cells, molecules ... More
Towards a theory of assembly of protein complexes: lessons from equilibrium statistical physicsJul 05 2019Cellular functions are established through biological evolution, but are constrained by the laws of physics. For instance, the physics of protein folding limits the lengths of cellular polypeptide chains. Consequently, many cellular functions are carried ... More
Intrinsic noise, Delta-Notch signalling and delayed reactions promote sustained, coherent, synchronised oscillations in the presomitic mesodermJun 21 2019Using a stochastic individual-based modelling approach, we examine the role that Delta-Notch signalling plays in the regulation of a robust and reliable somite segmentation clock. We find that not only can Delta-Notch signalling synchronise noisy cycles ... More
The quenched trap model on the extreme landscape: the rise of sub-diffusion and non-Gaussian diffusionJun 19 2019Non-Gaussian diffusion has been intensively studied in recent years, which reflects the dynamic heterogeneity in the disordered media. The recent study on the non-Gaussian diffusion in a static disordered landscape suggests novel phenomena due to the ... More
Stochastic thermodynamics and modes of operation of ribosome: A network theoretic perspectiveJun 19 2019The ribosome is one of the largest and most complex macromolecular machines in living cells. It polymerizes a specific protein in a step-by-step manner as directed by the corresponding template messenger RNA (mRNA) and this process is referred to as `translation' ... More
A mechanical model reveals that non-axisymmetric buckling lowers the energy barrier associated with membrane neck constrictionJun 15 2019Membrane neck formation is essential for scission, which, as recent experiments on tubules have demonstrated, can be location dependent. The diversity of biological machinery that can constrict a neck such as dynamin, actin, ESCRTs and BAR proteins, and ... More
Frequency and Time Domain Analysis ofsRNA-based Treatment for Inflammatory BowelDiseaseJun 12 2019The validity of a complex reaction pathway proposed to treat Inflammatory Bowel Disease (IBD) was verified by a comprehensive time and frequency domain analysis. The model was taken to the frequency domain to study the effect and the significance of the ... More
Cytoplasmic streaming in C. elegans: forces that drive oogenesisJun 07 2019In the gonad of C. elegans worms, germ cells form the outer lining of the central tube, the rachis, which carries a cytoplasmic flow. The porous interface between the germ cells and rachis allows a radial flow of cytoplasm across the interface. In the ... More
Cytoplasmic streaming in C. elegans: forces that drive oogenesisJun 07 2019Jun 13 2019In the gonad of C. elegans worms, germ cells form the outer lining of the central tube, the rachis, which carries a cytoplasmic flow.
Flexible Cancer-Associated Chromatin Configuration (CACC) Might Be the Fundamental Reason Why Cancer Is So Difficult to CureJun 06 2019Jun 16 2019We once proposed that cell-type-associated chromatin configurations determine cell types and that cancer cell type is determined by cancer-associated chromatin configuration (CACC). In this paper, we hypothesize that flexible cell-type-associated chromatin ... More
Flexible Cancer-Associated Chromatin Configuration (CACC) Might Be the Fundamental Reason Why Cancer Is So Difficult to CureJun 06 2019Jun 28 2019We once proposed that cell-type-associated chromatin configurations determine cell types and that cancer cell type is determined by cancer-associated chromatin configuration (CACC). In this paper, we hypothesize that flexible cell-type-associated chromatin ... More
Design and applications of a fluorescent labeling technique for lipid and surfactant preformed vesiclesJun 04 2019Amphiphilic molecules such as surfactants, lipids and block copolymers can be assembled into bilayers and form vesicles. Fluorescent membrane labeling methods require the use of dye molecules that can be inserted in the bilayers at different stages of ... More
Error-speed correlations in biopolymer synthesisMay 30 2019Synthesis of biopolymers such as DNA, RNA, and proteins are biophysical processes aided by enzymes. Performance of these enzymes is usually characterized in terms of their average error rate and speed. However, because of thermal fluctuations in these ... More
Search and capture efficiency of dynamic microtubules for centrosome relocation during IS formationMay 29 2019Upon contact with antigen presenting cells (APCs) cytotoxic T lymphocytes (T cells) establish a highly organized contact zone denoted as immunological synapse (IS). The formation of the IS implies relocation of the microtubule organizing center (MTOC) ... More
Microtubule Motility Analysis based on Time-Lapse Fluorescence MicroscopyMay 27 2019This paper describes an investigation into part of the mechanical mechanisms underlying the formation of mitotic spindle, the cellular machinery responsible for chromosomal separation during cell division. In normal eukaryotic cells, spindles are composed ... More
Cooperativity transitions driven by higher-order oligomer formations in ligand-induced receptor dimerizationMay 27 2019While cooperativity in ligand-induced receptor dimerization (e.g., EGF receptors) have been linked with receptor-receptor couplings via state-vector representations of physical observables, effects arising from higher-order oligomer formations of unobserved ... More
Optimal localization patterns in bacterial protein synthesisMay 25 2019In $\textit{Escherichia coli}$ bacterium, the molecular compounds involved in protein synthesis, messenger RNAs (mRNAs) and ribosomes, show marked intracellular localization patterns. Yet a quantitative understanding of the physical principles which would ... More
Stochastic Yield Catastrophes and Robustness in Self-AssemblyMay 23 2019A guiding principle in self-assembly is that, for high production yield, nucleation of structures must be significantly slower than their growth. However, details of the mechanism that impedes nucleation are broadly considered irrelevant. Here, we analyze ... More
Stress relaxation in F-actin solutions by severingMay 20 2019Jul 16 2019Networks of filamentous actin (F-actin) are important for the mechanics of most animal cells. These cytoskeletal networks are highly dynamic, with a variety of actin-associated proteins that control cross-linking, polymerization and force generation in ... More
Stress relaxation in F-actin solutions by severingMay 20 2019Networks of filamentous actin (F-actin) are important for the mechanics of most animal cells. These cytoskeletal networks are highly dynamic, with a variety of actin-associated proteins that control cross-linking, polymerization and force generation in ... More
Tunability of the Dual Feedback Genetic Oscillator Modeled by the Asymmetry in Transcription and TranslationMay 15 2019Oscillatory gene circuits are ubiquitous to biology and are involved in fundamental processes of cell cycle, circadian rhythms and developmental systems. The synthesis of small, non-natural oscillatory genetic circuits have been increasingly used to test ... More
Impact of global structure on diffusive exploration of planar networksMay 13 2019We investigate diffusive search on planar networks, motivated by tubular networks in cell biology that contain molecules searching for reaction partners and binding sites. Exact calculation of the diffusive mean first-passage time on a spatial network ... More
Effect of curvature and normal forces on motor regulation of ciliaMay 10 2019Cilia are ubiquitous organelles involves in eukaryotic motility. They are long, slender, and motile protrusions from the cell body. They undergo active regular oscillatory beating patterns that can propel cells, such as the algae Chlamydomonas, through ... More
Comparative approaches to understanding thyroid hormone regulation of neurogenesisMay 09 2019Thyroid hormone (TH) signalling, an evolutionary conserved pathway, is crucial for brain function and cognition throughout life, from early development to ageing. In humans, TH deficiency during pregnancy alters offspring brain development, increasing ... More
Tuning the Transdermal Transport by Application of External Continuous Electric Field: A Molecular Dynamics Coarse-Grained StudyMay 06 2019Since a long time the application of small electric potentials on biological membranes (iontophoresis) proved enabling control and improvement of transdermal delivery of substances across this barrier. In spite of a large experimental data, the detailed ... More
Mean velocity and effective diffusion constant for translocation of biopolymer chains across membraneMay 05 2019Chaperone-assisted translocation through a nanopore embedded in membrane holds a prominent role in the transport of biopolymers. Inspired by classical Brownian ratchet, we develop a theoretical framework characterizing such translocation process through ... More
Dynamics of particle uptake at cell membranesMay 03 2019Receptor-mediated endocytosis requires that the energy of adhesion overcomes the deformation energy of the plasma membrane. The resulting driving force is balanced by dissipative forces, leading to deterministic dynamical equations. While the shape of ... More
Stochastic Dynamics of Nanoparticle and Virus UptakeMay 03 2019The cellular uptake of nanoparticles or viruses requires that the gain of adhesion energy overcomes the cost of plasma membrane bending. It is well known that this leads to a minimal particle size for uptake. Using a simple deterministic theory for this ... More
A mechanism for sarcomere breathing: volume changes and advective flow within the myofilament latticeApr 29 2019During muscle contraction, myosin motors anchored on thick filaments bind to and slide actin thin filaments. These motors rely on ATP, supplied at the limits of diffusion from the sarcoplasm to the interior of the lattice of actin and myosin. Classic ... More
Collective dynamics of microtubule-based 3D active fluids from single microtubulesApr 26 2019Self-organization of kinesin-driven, microtubule-based 3D active fluids relies on the collective dynamics of single microtubules. However, the connection between macroscopic fluid flows and microscopic motion of microtubules remains unclear. In this work, ... More
Modelling Diffuse Subcellular Protein Structures as Dynamic Social NetworksApr 17 2019Fluorescence microscopy has led to impressive quantitative models and new insights gained from richer sets of biomedical imagery. However, there is a dearth of rigorous and established bioimaging strategies for modeling spatiotemporal behavior of diffuse, ... More
Load-dependent adaptation near zero load in the bacterial flagellar motorApr 11 2019The bacterial flagellar motor is an ion-powered transmembrane protein complex which drives swimming in many bacterial species. The motor consists of a cytoplasmic 'rotor' ring and a number of 'stator' units, which are rooted to the cell wall of the bacterium. ... More
Mechanical constraints influence microtubule orientation in plant cellsApr 08 2019In growing plant cells, parallel ordering of microtubules (MTs) along the inner surface of the cell membrane influences the direction of cell expansion and thereby plant morphology. For correct expansion of organs that primarily grow by elongating, such ... More
Molecular Self-Organization of Three-Component Lipid MembranesApr 03 2019By constructing a Landau-like energy functional, we investigate the molecular organization of a three-component mixture in cell membranes. In the strongly interacting limit, we model the interaction between molecules using pseudospin variables and convert ... More
How the Avidity of Polymerase Binding to the -35/-10 Promoter Sites Affects Gene ExpressionApr 03 2019Although the key promoter elements necessary to drive transcription in Escherichia coli have long been understood, we still cannot predict the behavior of arbitrary novel promoters, hampering our ability to characterize the myriad of sequenced regulatory ... More
Solvated Membrane Nanodiscoids: A Probe For The Effects Of Gaussian CurvatureApr 01 2019Several methods now exist to solvate lipid bilayer discoids at the scale of tens of nanometres. Due to their size, such nanodiscoids have a comparatively large boundary-to-area ratio, making them unusually well-suited to probing the effects of Gaussian ... More
The physical parameters of neuronal cargo transport regulated by autoinhibition of kinesin UNC-104Mar 29 2019In this review, we focus on the kinesin-3 family molecular motor protein UNC-104 and its regulatory protein ARL-8. UNC-104, originally identified in Caenorhabditis elegans (C. elegans), has a primary role transporting synaptic vesicle precursors (SVPs). ... More
Physical parameters describing neuronal cargo transport by kinesin UNC-104Mar 29 2019Apr 30 2019In this review, we focus on the kinesin-3 family molecular motor protein UNC-104 and its regulatory protein ARL-8. UNC-104, originally identified in Caenorhabditis elegans (C. elegans), has a primary role transporting synaptic vesicle precursors (SVPs). ... More
Modeling transport and mean age of dense core vesicles in large axonal arborsMar 25 2019May 02 2019A model simulating transport of dense core vesicles (DCVs) in type II axonal terminals of Drosophila motoneurons has been developed. An interesting feature of the morphology of type II terminals is the large number of en passant boutons. The lack of both ... More
Modeling transport and mean age of dense core vesicles in large axonal arborsMar 25 2019A model simulating transport of dense core vesicles (DCVs) in type II axonal terminals of Drosophila motoneurons has been developed. An interesting feature of the morphology of type II terminals is the large number of en passant boutons. The lack of both ... More
Ribosome flow model with different site sizesMar 12 2019We introduce and analyze two general dynamical models for unidirectional movement of particles along a circular chain and an open chain of sites. The models include a soft version of the simple exclusion principle, that is, as the density in a site increases ... More
Limited processivity of single motors improves overall transport flux of self-assembled motor-cargo complexesFeb 26 2019Single kinesin molecular motors can processively move along a microtubule (MT) a few micrometers on average before dissociating. However, cellular length scales over which transport occurs are several hundred microns and more. Why seemingly unreliable ... More
ABM of osteoblast's mechanotransduction pathway: time patterns of critical eventsFeb 23 2019Background: Mechanotransduction in bone cells plays a pivotal role in osteoblast differentiation and bone remodelling. Mechanotransduction provides the link between modulation of the extracellular matrix and intracellular actions. By controlling the balance ... More
Membrane morphologies induced by arc-shaped scaffolds are determined by arc angle and coverageFeb 22 2019The intricate shapes of biological membranes such as tubules and membrane stacks are induced by proteins. In this article, we systematically investigate the membrane shapes induced by arc-shaped scaffolds such as proteins and protein complexes with coarse-grained ... More
Diffusion through nanopores in connected lipid bilayer networksFeb 13 2019A biomimetic model of cell-cell communication was developed to probe the passive molecular transport across ion channels inserted in synthetic lipid bilayers formed between contacting droplets arranged in a linear array. Diffusion of a fluorescent probe ... More
How does interaction between RyR and IP3R mediated calcium release shape the calcium transient for hypertrophic signalling in cardiomyocytes?Feb 13 2019Calcium plays a central role in mediating both contractile function and hypertrophic signalling in cardiomyocytes. While L-type Ca2+ channels (LCCs) trigger beat-to-beat release of calcium through ryanodine receptors (RyRs) for cellular contraction, inositol ... More
IP3R Ca2+ release shapes the cytosolic Ca2+ transient for hypertrophic signalling in cardiomyocytesFeb 13 2019Mar 06 2019Calcium plays a central role in mediating both contractile function and hypertrophicsignalling in cardiomyocytes. While L-type Ca2+ channels (LCCs) trigger beat-to-beat re-lease of calcium through ryanodine receptors (RyRs) for cellular contraction, inositol ... More
Asymptotic behavior of the solution of the space dependent variable order fractional diffusion equation: ultra-slow anomalous aggregationFeb 08 2019We find for the first time the asymptotic representation of the solution to the space dependent variable order fractional diffusion and Fokker-Planck equations. We identify a new advection term that causes ultra-slow spatial aggregation of subdiffusive ... More
Magic numbers in polymer phase separation - the importance of being rigidJan 27 2019Cells possess non-membrane-bound bodies, many of which are now understood as phase-separated condensates. One class of such condensates is composed of two polymer species, where each consists of repeated binding sites that interact in a one-to-one fashion ... More
Spontaneous formation of chaotic protrusions in a polymerizing active gel layerJan 24 2019Apr 18 2019The actin cortex is a thin layer of actin filaments and myosin motors beneath the outer membrane of animal cells. It determines the cells' mechanical properties and forms important morphological structures. Physical descriptions of the cortex as a contractile ... More
Spontaneous formation of chaotic protrusions in a polymerizing active gel layerJan 24 2019The actin cortex is a thin layer of actin filaments and myosin motors beneath the outer membrane of animal cells. It determines the cells' mechanical properties and forms important morphological structures. Physical descriptions of the cortex as a contractile ... More
Spatial clustering and common regulatory elements correlate with coordinated gene expressionJan 18 2019Many cellular responses to surrounding cues require temporally concerted transcriptional regulation of multiple genes. In prokaryotic cells, a single-input-module motif with one transcription factor regulating multiple target genes can generate coordinated ... More
Centre-finding in E. coli and the role of mathematical modelling: past, present and futureJan 18 2019We review the key role played by mathematical modelling in elucidating two centre-finding patterning systems in E. coli: midcell division positioning by the MinCDE system and DNA partitioning by the ParABS system. We focus particularly on how, despite ... More
Diffusiophoresis in Cells: a General Non-Equilibrium, Non-Motor Mechanism for the Metabolism-Dependent Transport of Particles in CellsJan 03 2019Mar 04 2019The more we learn about the cytoplasm of cells, the more we realise that the cytoplasm is not uniform but instead is highly inhomogeneous. In any inhomogeneous solution, there are concentration gradients, and particles move either up or down these gradients ... More
Diffusiophoresis in Cells: a General Non-Equilibrium, Non-Motor Mechanism for the Metabolism-Dependent Transport of Particles in CellsJan 03 2019The more we learn about the cytoplasm of cells, the more we realise that the cytoplasm is not uniform but instead is highly inhomogeneous. In any inhomogeneous solution, there are concentration gradients, and particles move either up or down these gradients ... More
SIAN: software for structural identifiability analysis of ODE modelsDec 26 2018Biological processes are often modeled by ordinary differential equations with unknown parameters. The unknown parameters are usually estimated from experimental data. In some cases, due to the structure of the model, this estimation problem does not ... More
A biologically motivated three-species exclusion model: effects of leaky scanning and overlapping genes on initiation of protein synthesisDec 25 2018Totally asymmetric simple exclusion process (TASEP) was originally introduced as a model for the traffic-like collective movement of ribosomes on a messenger RNA (mRNA) that serves as the track for the motor-like forward stepping of individual ribosomes. ... More
A biologically motivated three-species exclusion model: effects of leaky scanning and overlapping genes on initiation of protein synthesisDec 25 2018Feb 08 2019Totally asymmetric simple exclusion process (TASEP) was originally introduced as a model for the traffic-like collective movement of ribosomes on a messenger RNA (mRNA) that serves as the track for the motor-like forward stepping of individual ribosomes. ... More
Controlling Organization and Forces in Active Matter Through Optically-Defined BoundariesDec 22 2018Jan 11 2019Living systems are capable of locomotion, reconfiguration, and replication. To perform these tasks, cells spatiotemporally coordinate the interactions of force-generating, "active" molecules that create and manipulate non-equilibrium structures and force ... More
Controlling Organization and Forces in Active Matter Through Optically-Defined BoundariesDec 22 2018May 24 2019Living systems are capable of locomotion, reconfiguration, and replication. To perform these tasks, cells spatiotemporally coordinate the interactions of force-generating, "active" molecules that create and manipulate non-equilibrium structures and force ... More
Theoretical Insights into Mechanisms of Stochastic Gating in Channel-Facilitated Molecular TransportDec 18 2018Molecular motion through pores plays a crucial role in various natural and industrial processes. One of the most fascinating features of biological channel-facilitated transport is a stochastic gating process, when the channels dynamically fluctuate between ... More
Breaking time-reversal symmetry for ratchet models of molecular machinesDec 18 2018May 29 2019Biomolecular machines transduce free energy from one form to another to fulfill many important roles inside cells, with dissipation required to achieve directed progress. We investigate how to break time-reversal symmetry at a given dissipation cost by ... More
Breaking time-reversal symmetry for ratchet models of molecular machinesDec 18 2018Biomolecular machines transduce free energy from one form to another to fulfill many important roles inside cells, with free energy dissipation required to achieve directed progress. We investigate how to break time-reversal symmetry at a given dissipation ... More
Dynamic anticipation by Cdk2/Cyclin A-bound p27 mediates signal integration in cell cycle regulationDec 17 2018p27$^{Kip1}$ (p27) is an intrinsically disordered protein (IDP) that folds upon binding to cyclin-dependent kinase (Cdk)$/$cyclin complexes (e.g., Cdk2$/$cyclin A), inhibiting their catalytic activity and causing cell cycle arrest. However, cell division ... More
Locally and Globally Optimal Configurations of $N$ Particles on the Sphere with Applications in the Narrow Escape and Narrow Capture ProblemsDec 15 2018Determination of \emph{optimal} arrangements of $N$ particles on a sphere is a well-known problem in physics. A famous example of such is the Thomson problem of finding equilibrium configurations of electrical charges on a sphere. More recently however, ... More
Murburn scheme for thermogenesis mediated by uncoupling proteinDec 14 2018Thermogenesis by uncoupling protein (UCP) has traditionally been explained as the dissipation of proton gradient across the inner mitochondrial membrane into heat. Herein, we propose that UCPs, aided by the large pore and positively charged amino acids ... More
Can a flux-based mechanism explain positioning of protein clusters in a three-dimensional cell geometry?Dec 14 2018The plane of bacterial cell division must be precisely positioned. In the bacterium Myxococcus xanthus, the proteins PomX and PomY form a large cluster, which is tethered to the nucleoid by the ATPase PomZ and moves in a stochastic, but biased manner ... More
The effect of the filament-obstacle interaction on the force-velocity relation of a growing biopolymerNov 30 2018We investigate the effect of filament-obstacle interactions on the force-velocity relation of growing biopolymers, via calculations explicitly treating obstacle diffusion and stochastic addition and subtraction of subunits. We first show that the subunit ... More
Speed-detachment tradeoff and its effect on track bound transport of single motor proteinNov 28 2018The transportation of the cargoes in biological cells is primarily driven by the motor proteins on filamentous protein tracks. The stochastic nature of the motion of motor protein often leads to its spontaneous detachment from the track. Using the available ... More
Towards a full quantitative description of single-molecule reaction kinetics in biological cellsNov 27 2018The first-passage time (FPT), i.e., the moment when a stochastic process reaches a given threshold value for the first time, is a fundamental mathematical concept with immediate applications. In particular, it quantifies the statistics of instances when ... More
Numerical parameter space compression and its application to microtubule dynamic instabilityNov 26 2018Physical models of biological systems can become difficult to interpret when they have a large number of parameters. But the models themselves actually depend on (i.e. are sensitive to) only a subset of those parameters. Rigorously identifying this subset ... More
Waveforms of molecular oscillations reveal circadian timekeeping mechanismsNov 26 2018Circadian clocks play a pivotal role in orchestrating numerous physiological and developmental events. Waveform shapes of the oscillations of protein abundances can be informative about the underlying biochemical processes of circadian clocks. We derive ... More
The Range of Cooperativity Modulates Actin Binding Protein Cluster Size, Density and DynamicsNov 23 2018The actin cytoskeleton is composed of multiple networks which are specialized for several processes such as cell motility or cell division. Each of these networks are composed of organized actin microfilaments which are decorated with specific sets of ... More
Direct Single Molecule Imaging of Enhanced Enzyme DiffusionNov 20 2018Recent experimental results have shown that active enzymes can diffuse faster when they are in the presence of their substrates. Fluorescence correlation spectroscopy (FCS), which relies on analyzing the fluctuations in fluorescence intensity signal to ... More
Surface reaction-diffusion kinetics on lattice at the microscopic scaleNov 17 2018Microscopic models of reaction-diffusion processes on the cell membrane can link local spatiotemporal effects to macroscopic self-organized patterns often observed on the membrane. Simulation schemes based on the microscopic lattice method (MLM) can model ... More
Optimality in self-organized molecular sortingNov 16 2018We introduce a simple physical picture to explain the process of molecule sorting, whereby specific proteins and lipids are concentrated and distilled into nanometric lipid vesicles in eukaryotic cells. To this purpose, we formulate a model based on the ... More
Extending the linear-noise approximation to biochemical systems influenced by intrinsic noise and slow lognormally distributed extrinsic noiseNov 14 2018It is well known that the kinetics of an intracellular biochemical network is stochastic. This is due to intrinsic noise arising from the random timing of biochemical reactions in the network as well as due to extrinsic noise stemming from the interaction ... More
Non-Markovian intracellular transport with sub-diffusion and run-length dependent detachment rateNov 04 2018Intracellular transport of organelles is fundamental to cell function and health. The mounting evidence suggests that this transport is in fact anomalous. However, the reasons for the anomaly is still under debate. We examined experimental trajectories ... More
Quantitative assessment of changes in cellular morphology at photodynamic treatment in vitro by means of digital holographic microscopyOct 30 2018Changes in morphological characteristics of cells from two cultured cancer cell lines, HeLa and A549, induced by photodynamic treatment with Radachlorin photosensitizer have been monitored using digital holographic microscopy. The observed dose-dependent ... More
MCell-R: A particle-resolution network-free spatial modeling frameworkOct 29 2018Spatial heterogeneity can have dramatic effects on the biochemical networks that drive cell regulation and decision-making. For this reason, a number of methods have been developed to model spatial heterogeneity and incorporated into widely used modeling ... More
A Biologically Motivated Asymmetric Exclusion Process: interplay of congestion in RNA polymerase traffic and slippage of nascent transcriptOct 27 2018We develope a theoretical framework, based on exclusion process, that is motivated by a biological phenomenon called transcript slippage (TS). In this model a discrete lattice repesents a DNA strand while each of the particles that hop on it unidirectionally, ... More
A Biologically Motivated Asymmetric Exclusion Process: interplay of congestion in RNA polymerase traffic and slippage of nascent transcriptOct 27 2018Apr 24 2019We develope a theoretical framework, based on exclusion process, that is motivated by a biological phenomenon called transcript slippage (TS). In this model a discrete lattice represents a DNA strand while each of the particles that hop on it unidirectionally, ... More
The $Ca^{2+}$-activated $Cl^-$ current ensures robust and reliable signal amplification in vertebrate olfactory receptor neuronsOct 25 2018Activation of most primary sensory neurons results in transduction currents that are carried by cations. One notable exception is the vertebrate olfactory receptor neuron (ORN), where the transduction current is carried largely by the anion $Cl^-$. However, ... More
Mechanical factors affecting the mobility of membrane proteinsOct 23 2018The mobility of membrane proteins controls many biological functions. The application of the model of Saffman and Delbr\"uck to the diffusion of membrane proteins does not account for all the experimental measurements. These discrepancies have triggered ... More
Active unidirectional network flow generates a packet molecular transport in cellsOct 16 2018Internet, social media, neuronal or blood vessel are organized in complex networks. These networks are characterized by several quantities such as the underlying graph connectivity (topology), how they grow in time, scaling laws or by the mean time a ... More