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Effects of high vs moderate-intensity training on neuroplasticity and functional recovery after focal ischemiaFeb 08 2018Background and Purpose: This study was designed to compare the effects of high-intensity interval training (HIT) and moderate-intensity continuous training (MOD) on functional recovery and cerebral plasticity during the first 2 weeks following cerebral ... More
PEBP1/RKIP: from multiple functions to a common role in cellular processesFeb 07 2018PEBPs (PhosphatidylEthanolamine Binding Proteins) form a protein family widely present in the living world since they are encountered in microorganisms, plants and animals. In all organisms PEBPs appear to regulate important mechanisms that govern cell ... 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
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
Generalizing Gillespie's direct method to enable network-free simulationsJan 30 2018Gillespie's direct method for stochastic simulation of chemical kinetics is a staple of computational systems biology research. However, the algorithm requires explicit enumeration of all reactions and all chemical species that may arise in the system. ... 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
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
Tuning transcriptional regulation through signaling: A predictive theory of allosteric inductionFeb 24 2017Jun 21 2017Allosteric regulation is found across all domains of life, yet we still lack simple, predictive theories that directly link the experimentally tunable parameters of a system to its input-output response. To that end, we present a general theory of allosteric ... 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
Mechanical Properties of TransriptionDec 07 2016Recently the physical characterization of a number of biological processes has proven indispensable for a full understanding of natural phenomena. One such example is the mechanical properties of transcription, which have been shown to have significant ... More
Regime shifts driven by dynamic correlations in gene expression noiseDec 04 2016Gene expression is a noisy process that leads to regime shift between alternative steady states among individual living cells, inducing phenotypic variability. The effects of white noise on the regime shift in bistable systems have been well characterized, ... More
Regime shifts driven by dynamic correlations in gene expression noiseDec 04 2016Dec 06 2016Gene expression is a noisy process that leads to regime shift between alternative steady states among individual living cells, inducing phenotypic variability. The effects of white noise on the regime shift in bistable systems have been well characterized, ... More
Dynamics in Steady State In Vitro Acto-Myosin NetworksNov 29 2016It is well known that many biochemical processes in the cell such as gene regulation, growth signals and activation of ion channels, rely on mechanical stimuli. However, the mechanism by which mechanical signals propagate through cells is not as well ... More
Thermodynamic competition between membrane protein oligomeric statesNov 28 2016Self-assembly of protein monomers into distinct membrane protein oligomers provides a general mechanism for diversity in the molecular architectures, and resulting biological functions, of membrane proteins. We develop a general physical framework describing ... More
Stochastic study of information transmission and population stability in a generic bacterial two-component systemNov 24 2016Studies on the role of fluctuations in signal propagation and on gene regulation in monoclonal bacterial population have been extensively pursued based on the machinery of two-component system. The bacterial two-component system shows noise utilisation ... More
Focal adhesion kinase - the reversible molecular mechanosensorNov 18 2016Sensors are the first element of the pathways that control the response of cells to their environment. After chemical, the next most important cue is mechanical, and protein complexes that produce or enable a chemical signal in response to a mechanical ... More
Toward a systems-level view of mitotic checkpointsNov 15 2016Reproduction and natural selection are the key elements of life. In order to reproduce, the genetic material must be doubled, separated and placed into two new daughter cells, each containing a complete set of chromosomes and organelles. In mitosis, transition ... More
An alternative approach to Michaelis-Menten kinetics that is based on the Renormalization Group: Comparison with the perturbation expansion beyond the sQSSANov 14 2016We recall the perturbation expansion for Michaelis-Menten kinetics, beyond the standard quasi-steady-state approximation (sQSSA). Against this background, we are able to appropriately apply the alternative approach to the study of singularly perturbed ... More
On the Mechanism of Homology Search by RecA Protein FilamentsNov 13 2016Genetic stability is a key factor in maintaining, survival and reproduction of biological cells. It relies on many processes, but one of the most important is a {\it homologous recombination}, in which the repair of breaks in double-stranded DNA molecules ... More
Dynamic instabilities in the kinetics of growth and disassembly of microtubulesNov 13 2016Dynamic instability of microtubules is considered using frameworks of non-linear thermodynamics and non-equilibrium reaction-diffusion systems. Stochastic assembly/disassembly phases in the polymerization dynamics of microtubules are treated as a result ... More
Sensitivity of small myosin II ensembles from different isoforms to mechanical load and ATP concentrationNov 09 2016Based on a detailed crossbridge model for individual myosin II motors, we systematically study the influence of mechanical load and adenosine triphosphate (ATP) concentration on small myosin II ensembles made from different isoforms. For skeletal and ... More
Architecture and Function of Mechanosensitive Membrane Protein LatticesNov 02 2016Experiments have revealed that membrane proteins can form two-dimensional clusters with regular translational and orientational protein arrangements, which may allow cells to modulate protein function. However, the physical mechanisms yielding supramolecular ... More
Signatures of protein structure in the cooperative gating of mechanosensitive ion channelsNov 02 2016Membrane proteins deform the surrounding lipid bilayer, which can lead to membrane-mediated interactions between neighboring proteins. Using the mechanosensitive channel of large conductance (MscL) as a model system, we demonstrate how the observed differences ... More
Automated scalable segmentation of neurons from multispectral imagesNov 01 2016Reconstruction of neuroanatomy is a fundamental problem in neuroscience. Stochastic expression of colors in individual cells is a promising tool, although its use in the nervous system has been limited due to various sources of variability in expression. ... More
Balance of microtubule stiffness and cortical tension determines the size of blood cells with marginal band across speciesOct 31 2016Nov 01 2016The fast blood stream of animals is associated with large shear stresses. Consequently, blood cells have evolved a special morphology and a specific internal architecture allowing them to maintain their integrity over several weeks. For instance, non-mammalian ... More
Balance of microtubule stiffness and cortical tension determines the size of blood cells with marginal band across speciesOct 31 2016The fast blood stream of animals is associated with large shear stresses. Consequently, blood cells have evolved a special morphology and a specific internal architecture allowing them to maintain their integrity over several weeks. For instance, non-mammalian ... More
Physical Basis of Large Microtubule Aster GrowthOct 31 2016Microtubule asters - radial arrays of microtubules organized by centrosomes - play a fundamental role in the spatial coordination of animal cells. The standard model of aster growth assumes a fixed number of microtubules originating from the centrosomes. ... More
Phosphorylation energy and nonlinear kinetics as key determinants for G2/M transition in fission yeast cell cycleOct 30 2016The living cell is an open nonequilibrium biochemical system, where ATP hydrolysis serves as the energy source for a wide range of intracellular processes including the assurance for decision-making. In the fission yeast cell cycle, the transition from ... More
Stochastic single-molecule dynamics of synaptic membrane protein domainsOct 29 2016Nov 07 2016Motivated by single-molecule experiments on synaptic membrane protein domains, we use a stochastic lattice model to study protein reaction and diffusion processes in crowded membranes. We find that the stochastic reaction-diffusion dynamics of synaptic ... More
Stochastic single-molecule dynamics of synaptic membrane protein domainsOct 29 2016Motivated by single-molecule experiments on synaptic membrane protein domains, we use a stochastic lattice model to study protein reaction and diffusion processes in crowded membranes. We find that the stochastic reaction-diffusion dynamics of synaptic ... More
Biophysical comparison of ATP-driven proton pumping mechanisms suggests a kinetic advantage for the rotary process depending on coupling ratioOct 28 2016ATP-driven proton pumps, which are critical to the operation of a cell, maintain cytosolic and organellar pH levels within a narrow functional range. These pumps employ two very different mechanisms: an elaborate rotary mechanism used by V-ATPase H+ pumps, ... More
Theory on the mechanisms of combinatorial binding of transcription factors with DNAOct 20 2016We develop a theoretical framework on the mechanism of combinatorial binding of transcription factors (TFs) with their specific binding sites on DNA. We consider three possible mechanisms viz. monomer, hetero-oligomer and coordinated recruitment pathways. ... More
Stochastic switching between multistable oscillation patterns of the Min-systemOct 17 2016The spatiotemporal oscillation patterns of the proteins MinD and MinE are used by the bacterium E. coli to sense its own geometry. Strikingly, both computer simulations and experiments have recently shown that for the same geometry of the reaction volume, ... More
Theory for strength and stability of an unusual "ligand-receptor" bond: a microtubule attached to a wall by molecular motor tethersOct 16 2016A microtubule (MT) is a tubular stiff filament formed by a hierarchical organization of tubulin proteins. We develop a stochastic kinetic model for studying the strength and stability of a pre-formed attachment of a MT with a rigid wall where the MT is ... More
A resource dependent protein synthesis model for evaluating synthetic circuitsOct 13 2016Reliable in-silico design of synthetic gene networks necessitates novel approaches to model the process of protein synthesis under the influence of limited resources. We present such a novel protein synthesis model which originates from the Ribosome Flow ... More
Geometric stability considerations of the ribosome flow model with poolOct 13 2016In order to better understand the process of gene translation, the ribosome flow model (RFM) with pool was introduced recently. This model describes the movement of several ribosomes along an mRNA template and simultaneously captures the dynamics of the ... More
Robustness analysis of spatiotemporal models in the presence of extrinsic fluctuationsOct 05 2016We analyze the governing partial differential equations of a model of pole-to-pole oscillations of the MinD protein in a bacterial cell. The sensitivity to extrinsic noise in the parameters of the model is explored. Our analysis shows that overall, the ... More
Tuning Multiple Motor Travel Via Single Motor VelocityOct 04 2016Microtubule-based molecular motors often work in small groups to transport cargos in cells. A key question in understanding transport (and its regulation in vivo) is to identify the sensitivity of multiple-motor-based motion to various single molecule ... More
Interplay between velocity and travel distance of kinesin-based transport in the presence of tauOct 04 2016Although the disease-relevant microtubule-associated protein tau is known to severely inhibit kinesin-based transport in vitro, the potential mechanisms for reversing this detrimental effect to maintain healthy transport in cells remain unknown. Here ... More
Microtubule Defects Influence Kinesin-Based Transport In VitroOct 04 2016Microtubules are protein polymers that form "molecular highways" for long-range transport within living cells. Molecular motors actively step along microtubules to shuttle cellular materials between the nucleus and the cell periphery; this transport is ... More
Quantitative Determination of the Probability of Multiple-Motor Transport in Bead-Based AssaysOct 04 2016With their longest dimension typically being less than 100 nm, molecular motors are significantly below the optical-resolution limit. Despite substantial advances in fluorescence-based imaging methodologies, labeling with beads remains critical for optical-trapping-based ... More
Modelling autophagy selectivity by receptor clustering on peroxisomesOct 03 2016When subcellular organelles are degraded by autophagy, typically some, but not all, of each targeted organelle type are degraded. Autophagy selectivity must not only select the correct type of organelle, but must discriminate between individual organelles ... More
Cooperative Protofilament Switching Emerges from Inter-Motor Interference in Multiple-Motor TransportOct 01 2016Within living cells, the transport of cargo is accomplished by groups of molecular motors. Such collective transport could utilize mechanisms which emerge from inter-motor interactions in ways that are yet to be fully understood. Here we combined experimental ... More
Wavy membranes and the growth rate of a planar chemical garden: Enhanced diffusion and bioenergeticsSep 26 2016In order to model ion transport across protocell membranes in Hadean hydrothermal vents, we consider both theoretically and experimentally the planar growth of a precipitate membrane formed at the interface between two parallel fluid streams in a two-dimensional ... More
Variance-corrected Michaelis-Menten equation predicts transient rates of single-enzyme reactions and response times in bacterial gene-regulationSep 26 2016Many chemical reactions in biological cells occur at very low concentrations of constituent molecules. Thus, transcriptional gene-regulation is often controlled by poorly expressed transcription-factors, such as E.coli lac repressor with few tens of copies. ... More
Effect of gene-expression bursts on stochastic timing of cellular eventsSep 23 2016Gene expression is inherently a noisy process which manifests as cell-to-cell variability in time evolution of proteins. Consequently, events that trigger at critical threshold levels of regulatory proteins exhibit stochasticity in their timing. An important ... More
Nonlinear self-adapting wave patternsSep 23 2016We propose a new type of traveling wave pattern, one that can adapt to the size of physical system in which it is embedded. Such a system arises when the initial state has an instability that extends down to zero wavevector, connecting at that point to ... More
A Deterministic Mathematical Model for Bidirectional Excluded Flow with Langmuir KineticsSep 19 2016In many important cellular processes, including mRNA translation, gene transcription, phosphotransfer, and intracellular transport, biological "particles" move along some kind of "tracks". The motion of these particles can be modeled as a one-dimensional ... More
Membrane tubulation by elongated and patchy nanoparticlesSep 15 2016Advances in nanotechnology lead to an increasing interest in how nanoparticles interact with biomembranes. Nanoparticles are wrapped spontaneously by biomembranes if the adhesive interactions between the particles and membranes compensate for the cost ... More
Scale dependence of mechanics and dynamics of active gels with increasing motor concentrationSep 14 2016The cytoskeleton protein actin assembles into large bundles when supporting stresses in the cell, but grows into a fine branched network to induce cell motion. Such self-organization processes are studied in artificial networks of cytoskeleton proteins ... More
Sets of FCS experiments to quantify free diffusion coefficients in reaction-diffusion systems. The case of Ca2+ and its dyesSep 13 2016Many cell signaling pathways involve the diffusion of messengers that bind/unbind to intracellular components. Quantifying their net transport rate under different conditions, then requires having separate estimates of their free diffusion coefficient ... More
Purification of recombinant human and Drosophila septin hexamers for TIRF assays of actin-septin filament assemblySep 13 2016Septins are guanine nucleotide-binding proteins that are conserved from fungi to humans. Septins assemble into heterooligomeric complexes and higher-order structures with key roles in various cellular functions including cell migration and division. The ... More
Visualizing septins in early Drosophila embryosSep 13 2016Functional studies in Drosophila have been key for establishing a role for the septin family of proteins in animal cell division and thus extending for the first time observations from the budding yeast to animal cells. Visualizing the distribution of ... More
Non-equilibrium fluctuations of a semi-flexible filament driven by active cross-linkersSep 02 2016The cytoskeleton is an inhomogeneous network of semi-flexible filaments, which are involved in a wide variety of active biological processes. Although the cytoskeletal filaments can be very stiff and embedded in a dense and cross-linked network, it has ... More
Pattern formation in polymerising actin flocks: spirals, spots and waves without nonlinear chemistryAug 25 2016Aug 26 2016We propose a model solely based on actin treadmilling and polymerisation which describes many characteristic states of actin wave formation: spots, spirals and travelling waves. In our model, as in experiments on cell recovering motility following actin ... More
Time-dependent solutions for a stochastic model of gene expression with molecule production in the form of a compound Poisson processAug 25 2016We study a stochastic model of gene expression, in which protein production has a form of random bursts whose size distribution is arbitrary, whereas protein decay is a first-order reaction. We find exact analytical expressions for the time evolution ... More
The Role of the Hes1 Crosstalk Hub in Notch-Wnt Interactions of the Intestinal CryptAug 22 2016The Notch pathway plays a vital role in determining whether cells in the intestinal epithelium adopt a secretory or an absorptive phenotype. Cell fate specification is coordinated via Notch's interaction with the canonical Wnt pathway. Here, we propose ... More
Pulsatile lipid vesicles under osmotic stressAug 18 2016The response of lipid bilayers to osmotic stress is an important part of cellular function. Previously, in [Oglecka et al. 2014], we reported that cell-sized giant unilamellar vesicles (GUVs) exposed to hypotonic media, respond to the osmotic assault ... More
Dopamine modulation of prefrontal delay activity-reverberatory activity and sharpness of tuning curvesAug 16 2016Recent electrophysiological experiments have shown that dopamine (D1) modulation of pyramidal cells in prefrontal cortex reduces spike frequency adaptation and enhances NMDA transmission. Using four models, from multicompartmental to integrate and fire, ... More
Emergence of Dynamic Cooperativity in the Stochastic Kinetics of Fluctuating EnzymesAug 11 2016Dynamic cooperativity in monomeric enzymes is characterized in terms of a non-Michaelis-Menten kinetic behaviour. The latter is believed to be associated with mechanisms that include multiple reaction pathways due to enzymatic conformational fluctuations. ... More
Computational Limitations of First-Order Repressor SystemsAug 10 2016Almost all current approaches for engineering modular logic components in synthetic biology use first-order regulators, including most CRISPR/CAS, TAL, zinc finger, and RNA interference systems. Many practitioners understand intuitively that second and ... More
Genoautotomy (Genome 'Self-Injury') in Eukaryotic Cells: A Cellular Defence Response to Genotoxic StressAug 02 2016Aug 18 2016This paper proposes that eukaryotic cells, under severe genotoxic stress, can commit genoautotomy (genome 'self-injury') that involves cutting and releasing single-stranded DNA (ssDNA) fragments from double-stranded DNA and leaving ssDNA gaps in the genome. ... More
Mitochondrial Ca2+ uptake in skeletal muscle health and diseaseJul 28 2016Muscle uses Ca2+ as a messenger to control contraction and relies on ATP to maintain the intracellular Ca2+ homeostasis. Mitochondria are the major sub-cellular organelle of ATP production. With a negative inner membrane potential, mitochondria take up ... More
Modeling of Ribosome Dynamics on a ds-mRNA under an External LoadJul 25 2016Protein molecules in cells are synthesized by macromolecular machines called ribosomes. According to recent experimental data, we reduce the complexity of the ribosome and propose a model to express its activity in six main states. Using our model, we ... More
Allosteric Regulation by a Critical MembraneJul 22 2016Many of the processes that underly neural computation are carried out by ion channels embedded in the plasma membrane, a two-dimensional liquid that surrounds all cells. Recent experiments have demonstrated that this membrane is poised close to a liquid-liquid ... More
Ephemeral protein binding to DNA shapes stable nuclear bodies and chromatin domainsJul 22 2016Fluorescence microscopy reveals that the contents of many (membrane-free) nuclear "bodies" exchange rapidly with the soluble pool whilst the underlying structure persists; such observations await a satisfactory biophysical explanation. To shed light on ... More
Mechanosensing in myosin filament solves a 60 years old conflict in skeletal muscle modeling between high power output and slow rise in tensionJul 20 2016Almost 60 years ago Andrew Huxley with his seminal paper \cite{Huxley1957} laid the foundation of modern muscle modeling, linking chemical events to mechanical performance. He described mechanics and energetics of muscle contraction through the cyclical ... More
A nonequilibrium diffusion and capture mechanism ensures tip-localization of regulating proteins on dynamic filamentsJul 18 2016Diffusive motion of regulatory enzymes on biopolymers with eventual capture at a reaction site is a common feature in cell biology. Using a lattice gas model we study the impact of diffusion and capture for a microtubule polymerase and a depolymerase. ... More
Theory for transitions between log and stationary phases: universal laws for lag timeJul 12 2016Quantitative characterization of bacterial growth has gathered substantial attention since Monod's pioneering study. Theoretical and experimental work has uncovered several laws for describing the log growth phase, in which the number of cells grows exponentially. ... More
Narrow escape to small windows on a small ball modeling the viral entry into the cell nucleusJul 08 2016Jul 18 2016A certain class of viruses replicates inside a cell if they can enter the nucleus through one of many small target pores, before being permanently trapped or degraded. We adopt for viral motion a switching stochastic process model and we estimate here ... More
Stochastic Models of Vesicular Sorting in Cellular OrganellesJun 28 2016The proper sorting of membrane components by regulated exchange between cellular organelles is crucial to intra-cellular organization. This process relies on the budding and fusion of transport vesicles, and should be strongly influenced by stochastic ... More
Law of localization in chemical reaction networksJun 28 2016Jul 04 2016In living cells, chemical reactions are connected by sharing their products and substrates, and form complex networks, e.g. metabolic pathways. Here we developed a theory to predict the sensitivity, i.e. the responses of concentrations and fluxes to perturbations ... More
Contributions of microtubule dynamic instability and rotational diffusion to kinetochore captureJun 24 2016Microtubule dynamic instability allows search and capture of kinetochores during spindle formation, an important process for accurate chromosome segregation during cell division. Recent work has found that microtubule rotational diffusion about minus-end ... More
Actin filaments growing against a barrier with fluctuating shapeJun 24 2016We study force generation by a set of parallel actin filaments growing against a non-rigid obstacle, in presence of an external load. The filaments polymerize by either moving the whole obstacle, with a large energy cost, or by causing local distortion ... More
Stochastic models of the binding kinetics of VEGF-A to VEGFR1 and VEGFR2 in endothelial cellsJun 23 2016Vascular endothelial growth factor receptors (VEGFRs) are receptor tyrosine kinases (RTKs) that regulate proliferation, migration, angiogenesis and vascular permeability of endothelial cells. VEGFR1 and VEGFR2 bind vascular endothelial growth factors ... More
Effects of initial telomere length distribution on senescence onset and heterogeneityJun 22 2016Nov 07 2016Replicative senescence, induced by telomere shortening, exhibits considerable asynchrony and heterogeneity, the origins of which remain unclear. Here, we formally study how telomere shortening mechanisms impact on senescence kinetics and define two regimes ... More
Effects of initial telomere length distribution on senescence onset and heterogeneityJun 22 2016Replicative senescence, induced by telomere shortening, exhibits considerable asynchrony and heterogeneity, the origins of which remain unclear. Here, we formally study how telomere shortening mechanisms impact on senescence kinetics and define two regimes ... More
A stochastic model of supercoiling-dependent transcriptionJun 21 2016Jun 29 2016We propose a stochastic model for gene transcription coupled to DNA supercoiling, where we incorporate the experimental observation that polymerases create supercoiling as they unwind the DNA helix, and that these enzymes bind more favourably to regions ... More
How does a protein reach its binding locus: sliding along DNA chain or not?Jun 17 2016In gene expression, various kinds of proteins need to bind to specific locus of DNA. It is still not clear how these proteins find their target locus. In this study, the mean first-passage time (FPT) of protein binding to its target locus on DNA chain ... More
From Conformational Spread to Allosteric and Cooperative models of E. coli flagellar motorJun 14 2016Sep 29 2016Escherichia coli swims using flagella activated by rotary motors. The direction of rotation of the motors is indirectly regulated by the binding of a single messenger protein. The conformational spread model has been shown to accurately describe the equilibrium ... More
Binding equilibrium and kinetics of membrane-anchored receptors and ligands in cell adhesion: insights from computational model systems and theoryJun 14 2016The adhesion of cell membranes is mediated by the binding of membrane-anchored receptor and ligand proteins. In this article, we review recent results from simulations and theory that lead to novel insights on how the binding equilibrium and kinetics ... More
Mechanical stability of bipolar spindle assemblyJun 14 2016Assembly and stability of mitotic spindle is governed by the interplay of various intra-cellular forces, e.g. the forces generated by motor proteins by sliding overlapping anti-parallel microtubules (MTs) polymerized from the opposite centrosomes, the ... More
Landau Theory and the Emergence of Chirality in Viral CapsidsJun 08 2016We present a generalized Landau-Brazovskii theory for the solidification of chiral molecules on a spherical surface. With increasing sphere radius one encounters first intervals where robust achiral density modulations appear with icosahedral symmetry ... More
Run-and-tumble dynamics of cytoskeletal motor proteinsJun 07 2016Cytoskeletal motor proteins are involved in major intracellular transport processes which are vital for maintaining appropriate cellular function. The motor exhibits distinct states of motility: active motion along filaments, and effectively stationary ... More
Run-and-pause dynamics of cytoskeletal motor proteinsJun 07 2016Nov 28 2016Cytoskeletal motor proteins are involved in major intracellular transport processes which are vital for maintaining appropriate cellular function. The motor exhibits distinct states of motility: active motion along filaments, and effectively stationary ... More
Small-volume effect enables the spine robust, sensitive and efficient information transferJun 07 2016Why is the spine of a neuron so small that only small numbers of molecules can exist and reactions inevitably become stochastic? Despite such noisy conditions, we previously showed that the spine exhibits robust, sensitive and efficient features of information ... More
Nonequilibrium mechanisms underlying de novo biogenesis of Golgi cisternaeJun 06 2016A central issue in cell biology is the physico-chemical basis of organelle biogenesis in intracellular trafficking pathways, its most impressive manifestation being the biogenesis of Golgi cisternae. At a basic level, such morphologically and chemically ... More
Stochastic Model of Maturation and Vesicular Exchange in Cellular OrganellesJun 03 2016The dynamical organization of membrane-bound organelles along intracellular transport pathways relies on vesicular exchange between organelles and on biochemical maturation of the organelle content by specific enzymes. The relative importance of each ... More
Theory on the mechanism of site-specific DNA-protein interactions in the presence of trapsMay 31 2016The speed of site-specific binding of transcription factor (TFs) proteins with genomic DNA seems to be strongly retarded by the randomly occurring sequence traps. Traps are those DNA sequences sharing significant similarity with the original specific ... More
Spatial Organization of the Cytoskeleton enhances Cargo Delivery to Specific Target Areas on the Plasma Membrane of Spherical CellsMay 30 2016Intracellular transport is vital for the proper functioning and survival of a cell. Cargo (proteins, vesicles, organelles, etc.) is transferred from its place of creation to its target locations via molecular motor assisted transport along cytoskeletal ... More
Spatial Organization of the Cytoskeleton enhances Cargo Delivery to Specific Target Areas on the Plasma Membrane of Spherical CellsMay 30 2016Nov 16 2016Intracellular transport is vital for the proper functioning and survival of a cell. Cargo (proteins, vesicles, organelles, etc.) is transferred from its place of creation to its target locations via molecular motor assisted transport along cytoskeletal ... More
Theory of dynamic force spectroscopy for kinetochore-microtubule attachments: rupture force distributionMay 28 2016Application of pulling force, under force-clamp conditions, to kinetochore-microtubule attachments {\it in-vitro} revealed a catch-bond-like behavior. In an earlier paper ({\it Sharma et al. Phys. Biol. (2014)} the physical origin of this apparently counter-intuitive ... More
Single molecule narrowfield microscopy of protein-DNA binding dynamics in glucose signal transduction of live yeast cellsMay 25 2016Single-molecule narrowfield microscopy is a versatile tool to investigate a diverse range of protein dynamics in live cells and has been extensively used in bacteria. Here, we describe how these methods can be extended to larger eukaryotic, yeast cells, ... More
Using Fluorescence Recovery After Photobleaching (FRAP) to study dynamics of the Structural Maintenance of Chromosome (SMC) complex in vivoMay 25 2016The SMC complex, MukBEF, is important for chromosome organization and segregation in Escherichia coli. Fluorescently tagged MukBEF forms distinct spots (or 'foci') in the cell, where it is thought to carry out most of its chromosome associated activities. ... More
Single-molecule observation of DNA replication repair pathways in E. coliMay 25 2016The method of action of many antibiotics is to interfere with DNA replication - quinolones trap DNA gyrase and topoisomerase proteins onto DNA while metronidazole causes single and double stranded breaks in DNA. To understand how bacteria respond to these ... More
Hybrid Markov-mass action law for cell activation by rare binding eventsMay 24 2016The binding of molecules, ions or proteins to specific target sites is a generic step for cell activation. However, this step relies on rare events where stochastic particles located in a large bulk are searching for small and often hidden targets and ... More
The mitotic spindle in the one-cell C. elegans embryo is positioned with high precision and stabilityMay 23 2016Sep 13 2016Precise positioning of the mitotic spindle is important for specifying the plane of cell division, which in turn determines how the cytoplasmic contents are partitioned into the daughter cells, and how the daughters are positioned within the tissue. During ... More
Bidirectionality From Cargo Thermal Fluctuations in Motor-Mediated TransportMay 20 2016Molecular motor proteins serve as an essential component of intracellular transport by generating forces to haul cargoes along cytoskeletal filaments. In some circumstances, two species of motors that are directed oppositely (e.g. kinesin, dynein) can ... More
Bidirectionality From Cargo Thermal Fluctuations in Motor-Mediated TransportMay 20 2016Oct 22 2016Molecular motor proteins serve as an essential component of intracellular transport by generating forces to haul cargoes along cytoskeletal filaments. Two species of motors that are directed oppositely (e.g. kinesin, dynein) can be attached to the same ... More