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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 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 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
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
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
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 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
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
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
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
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
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
Translocatome: a novel resource for the analysis of protein translocation between cellular organellesOct 15 2018Jan 15 2019Here we present Translocatome, the first dedicated database of human translocating proteins. The core of the Translocatome database is the manually curated data set of 213 human translocating proteins listing the source of their experimental validation, ... More
Receptor crosstalk improves concentration sensing of multiple ligandsOct 10 2018Cells need to reliably sense external ligand concentrations to achieve various biological functions such as chemotaxis or signaling. The molecular recognition of ligands by surface receptors is degenerate in many systems leading to crosstalk between different ... More
Synthesis for Vesicle Traffic SystemsOct 10 2018Vesicle Traffic Systems (VTSs) are the material transport mechanisms among the compartments inside the biological cells. The compartments are viewed as nodes that are labeled with the containing chemicals and the transport channels are similarly viewed ... More
Most Probable Evolution Trajectories in a Genetic Regulatory System Excited by Stable Lévy NoiseOct 09 2018Jan 28 2019We study the most probable trajectories of the concentration evolution for the transcription factor activator in a genetic regulation system, with non-Gaussian stable L\'evy noise in the synthesis reaction rate taking into account. We calculate the most ... More
Autoamplification and competition drive symmetry breaking: Initiation of centriole duplication by the PLK4-STIL networkSep 28 2018Symmetry breaking, a central principle of physics, has been hailed as the driver of self-organization in biological systems in general and biogenesis of cellular organelles in particular, but the molecular mechanisms of symmetry breaking only begin to ... More
Stochastic Simulation to Visualize Gene Expression and Error Correction in Living CellsSep 15 2018Stochastic simulation can make the molecular processes of cellular control more vivid than the traditional differential-equation approach by generating typical system histories instead of just statistical measures such as the mean and variance of a population. ... More
Spatial control of irreversible protein aggregationSep 10 2018Liquid cellular compartments spatially segregate from the cytoplasm and can regulate aberrant protein aggregation, a process linked to several medical conditions, including Alzheimer's and Parkinson's diseases. Yet the mechanisms by which these droplet-like ... More
Mitochondrial network fragmentation modulates mutant mtDNA accumulation independently of absolute fission-fusion ratesSep 06 2018Mitochondrial DNA (mtDNA) mutations cause severe congenital diseases but may also be associated with healthy aging. MtDNA is stochastically replicated and degraded, and exists within organelles which undergo dynamic fusion and fission. The role of the ... More
Mitochondrial heterogeneitySep 06 2018Dec 18 2018Cell-to-cell heterogeneity drives a range of (patho)physiologically important phenomena, such as cell fate and chemotherapeutic resistance. The role of metabolism, and particularly mitochondria, is increasingly being recognised as an important explanatory ... More
Is Actin Filament and Microtubule Growth Reaction- or Diffusion-Limited?Aug 29 2018Inside cells of living organisms, actin filaments and microtubules self-assemble and dissemble dynamically by incorporating actin or tubulin from the cell plasma or releasing it into their tips' surroundings. Such reaction-diffusion systems can show diffusion- ... More
Mechanisms of Protein Search for Targets on DNA: Theoretical InsightsAug 03 2018Protein-DNA interactions are critical for the successful functioning of all natural systems. The key role in these interactions is played by processes of protein search for specific sites on DNA. Although it has been studied for many years, only recently ... More
Protein escape at the ribosomal exit tunnel: Effects of native interactions, tunnel length and macromolecular crowdingJul 26 2018How fast a post-translational nascent protein escapes from the ribosomal exit tunnel is relevant to its folding and protection against aggregation. Here, by using Langevin molecular dynamics, we show that non-local native interactions help decreasing ... More
Multiparametric qualimetric microsurgical scanning chip-lancet model: theoretical metrological and biomedical considerationsJul 23 2018The construction of a novel surgical instrument is considered, which is also a probing device providing a signal to the measuring equipment, which after its interpretation allows to obtain useful information about the section quality and the biomaterial ... More
Can graphene bilayers be the membrane mimetic materials? "Ion channels" in graphene-based nanostructuresJul 23 2018The prospects of application of graphene and related structures as the membrane mimetic materials, capable of reproducing several biomembrane functions up to the certain limit, are analyzed in the series of our papers. This paper considers the possibility ... More
A simple device for microinjections, manipulations and measurements using an electromorphological chip under microinterferometric control of the interface and membrane processes at the thickness range of 5-1000 nm at different anglesJul 23 2018Micromanipulations, perfusions and measurements performed using glass microelectrodes filled with an electrolyte is a conventional technique for experimental morphological and membrane electrophysiological studies at a single cell and membrane surface ... More
Can you hear an axon growing?Jul 12 2018Nov 02 2018Axons are linear processes of nerve cells that can range from a few tens of micrometers up to meters in length. In addition to external cues, the length of an axon is also regulated by unknown internal mechanisms. Molecular motors have been suggested ... More
Multistationarity and Bistability for Fewnomial Chemical Reaction NetworksJul 09 2018Dec 03 2018Bistability and multistationarity are properties of reaction networks linked to switch-like responses and connected to cell memory and cell decision making. Determining whether and when a network exhibits bistability is a hard and open mathematical problem. ... More
Abnormal Calcium Leak from Cardiac Sarcoplasmic Reticulum: New Insights Offered by Statistical PhysicsJul 04 2018Rationale: Heart muscle contraction is activated by a synchronized systolic Ca release from sarcoplasmic reticulum (SR) via Ca sparks. In disease, Ca sparks fail to terminate, causing a diastolic Ca leak that decreases contraction amplitude and increases ... More
Nanopore occlusion: A biophysical mechanism for bipolar cancellation in cell membranesJul 03 2018Extraordinarily large but short electric field pulses are reported by many experiments to cause bipolar cancellation (BPC). This unusual cell response occurs if a first pulse is followed by a second pulse with opposite polarity. Possibly universal, BPC ... More
Force-dependent unbinding rate of molecular motors from stationary optical trap dataJun 20 2018Molecular motors walk along filaments until they detach stochastically with a force-dependent unbinding rate. Here, we show that this unbinding rate can be obtained from the analysis of experimental data of molecular motors moving in stationary optical ... More
Designing diagnostic platforms for analysis of disease patterns and probing disease emergenceJun 17 2018The emerging era of personalized medicine relies on medical decisions, practices, and products being tailored to the individual patient. Point-of-care systems, at the heart of this model, play two important roles. First, they are required for identifying ... More
Modeling of drug diffusion in a solid tumor leading to tumor cell deathJun 05 2018It has been shown recently that changing the fluidic properties of a drug can improve its efficacy in ablating solid tumors. We develop a modeling framework for tumor ablation, and present the simplest possible model for drug diffusion in a spherical ... More
Memory effects and Lévy walk dynamics in intracellular transport of cargoesJun 01 2018Oct 25 2018We demonstrate the phenomenon of cumulative inertia in intracellular transport involving multiple motor proteins in human epithelial cells by measuring the empirical survival probability of cargoes on the microtubule and their detachment rates. We found ... More
Saikosaponins with similar structures but different mechanisms lead to combined hepatotoxicityMay 14 2018Radix Bupleuri is a hepatoprotective traditional Chinese medicine (TCM) used for thousands of years in clinical, which was reported to be linked with liver damage. Previous studies have revealed that saikosaponins are the major types of components that ... More
Fiber plucking by molecular motors yields large emergent contractility in stiff biopolymer networksMay 12 2018The mechanical properties of the cell depend crucially on the tension of its cytoskeleton, a biopolymer network that is put under stress by active motor proteins. While the fibrous nature of the network is known to strongly affect the transmission of ... More
Quantifying the Sensitivity of HIV-1 Viral Entry to Receptor and Coreceptor ExpressionMay 08 2018Infection by many viruses begins with fusion of viral and cellular lipid membranes, followed by entry of viral contents into the target cell and ultimately, after many biochemical steps, integration of viral DNA into that of the host cell. The early steps ... More
Stress-dependent amplification of active forces in nonlinear elastic mediaMay 07 2018The production of mechanical stresses in living organisms largely relies on localized, force-generating active units embedded in filamentous matrices. Numerical simulations of discrete fiber networks with fixed boundaries have shown that buckling in the ... More
Kinetics of Protein-DNA Interactions: First-Passage AnalysisApr 26 2018All living systems can function only far away from equilibrium, and for this reason chemical kinetic methods are critically important for uncovering the mechanisms of biological processes. Here we present a new theoretical method of investigating dynamics ... More
The mre11 A470 alleles influence the hereditability and the segregation of telosomes in Saccharomyces cerevisiae (original with corrected raw data)Apr 26 2018Apr 30 2018Telomeres, the nucleoprotein complexes at the termini of linear chromosomes, are essential for the processes of end replication, end protection, and chromatin segregation. The Mre11 complex is involved in multiple cellular roles in DNA repair and structure ... More
Large-scale chirality in an active layer of microtubules and kinesin motor proteinsApr 03 2018During the early developmental process of organisms, the formation of the left-right laterality requires a subtle mechanism, as it is associated with other principal body axes. Any inherent chiral feature in an egg cell can in principal trigger this spontaneous ... More
Curvature-sensitive kinesin binding can explain microtubule ring formation and reveals chaotic dynamics in a mathematical modelMar 20 2018Aug 01 2018Microtubules are filamentous tubular protein polymers which are essential for a range of cellular behaviour, and are generally straight over micron length scales. However, in some gliding assays, where microtubules move over a carpet of molecular motors, ... More
pH Sensing by Lipids in Membranes: The Fundamentals of pH-driven Migration, Polarization and Deformations of Lipid Bilayer AssembliesMar 15 2018Most biological molecules contain acido-basic groups that modulate their structure and interactions. A consequence is that pH gradients, local heterogeneities and dynamic variations are used by cells and organisms to drive or regulate specific biological ... More
The signaling signature of the neurotensin type 1 receptor with endogenous ligandsMar 12 2018Mar 14 2018The human neurotensin 1 receptor (hNTS1) is a G protein-coupled receptor involved in many physiological functions, including analgesia, hypothermia, and hypotension. To gain a better understanding of which signaling pathways or combination of pathways ... More
Universal kinetics for engagement of mechanosensing pathways in cell adhesionMar 12 2018Oct 04 2018When plated onto substrates, cell morphology and even stem cell differentiation are influenced by the stiffness of their environment. Stiffer substrates give strongly spread (eventually polarized) cells with strong focal adhesions, and stress fibers; ... More
Existence and stability of periodic solutions of an impulsive differential equation and application to CD8 T-cell differentiationMar 05 2018Unequal partitioning of the molecular content at cell division has been shown to be a source of heterogeneity in a cell population. We propose to model this phenomenon with the help of a scalar, nonlinear impulsive differential equation (IDE). In a first ... More
Limited Resources Induce Bistability in Microtubule Length RegulationFeb 26 2018Apr 09 2018The availability of protein is an important factor for the determination of the size of the mitotic spindle. Involved in spindle-size regulation is kinesin-8, a molecular motor and microtubule (MT) depolymerase, which is known to tightly control MT length. ... More
Collective Dynamics of Self-propelled Semiflexible FilamentsFeb 21 2018The collective behavior of active semiflexible filaments is studied with a model of tangentially driven self-propelled worm-like chains. The combination of excluded-volume interactions and self-propulsion leads to several distinct dynamic phases as a ... More
Self-organization principles of intracellular pattern formationFeb 20 2018Dynamic patterning of specific proteins is essential for the spatiotemporal regulation of many important intracellular processes in procaryotes, eucaryotes, and multicellular organisms. The emergence of patterns generated by interactions of diffusing ... More
Bond graph modelling of the cardiac action potential: Implications for drift and non-unique steady statesFeb 13 2018Mathematical models of cardiac action potentials have become increasingly important in the study of heart disease and pharmacology, but concerns linger over their robustness during long periods of simulation, in particular due to issues such as model ... More
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
In silico evolution of signaling networks using rule-based models: bistable response dynamicsFeb 01 2018Feb 06 2018One of the ultimate goals in biology is to understand the design principles of biological systems. Such principles, if they exist, can help us better understand complex, natural biological systems and guide the engineering of de novo ones. Towards deciphering ... 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
Design principles and optimal performance for molecular motors under realistic constraintsJan 29 2018The performance of a molecular motor, characterized by its power output and energy efficiency, is investigated in the motor design space spanned by the stepping rate function and the motor-track interaction potential. Analytic results and simulations ... More
Dynein catch bond as a mediator of codependent bidirectional cellular transportJan 21 2018Intracellular bidirectional transport of cargo on Microtubule filaments is achieved by the collective action of oppositely directed dynein and kinesin motors. Experimental investigations probing the nature of bidirectional transport have found that in ... More
Protein Pattern FormationJan 04 2018Feb 20 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
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
Cargo binding promotes KDEL receptor clustering at the mammalian cell surfaceDec 17 2017Transmembrane receptor clustering is a ubiquitous phenomenon in pro- and eukaryotic cells to physically sense receptor/ligand interactions and subsequently translate an exogenous signal into a cellular response. Despite that receptor cluster formation ... 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
Non-Gaussian diffusion in static disordered mediaDec 02 2017Mar 24 2018Non-Gaussian diffusion is commonly considered as a result of fluctuating diffusivity, which is correlated in time or in space or both. In this work, we investigate the non-Gaussian diffusion in static disordered media via a quenched trap model, where ... More
Decoupled molecules with binding polynomials of bidegree (n,2)Nov 18 2017We present a result on the number of decoupled molecules for systems binding two different types of ligands. In the case of $n$ and $2$ binding sites respectively, we show that, generically, there are $2(n!)^{2}$ decoupled molecules with the same binding ... More
Analysis of non-processive molecular motor transport using renewal reward theoryNov 13 2017Sep 27 2018We propose and analyze a mathematical model of cargo transport by non-processive molecular motors. In our model, the motors change states by random discrete events (corresponding to stepping and binding/unbinding), while the cargo position follows a stochastic ... More
Do cells sense time by number of divisions?Nov 12 2017Do biological cells sense time by the number of their divisions, a process that ends at senescence? We consider the question "can the cell's perception of time be expressed through the length of the shortest telomere?" The answer is that the absolute ... More
Asymptotics of extreme statistics of escape time in 1,2 and 3-dimensional diffusionsOct 29 2017The first of $N$ identical independently distributed (i.i.d.) Brownian trajectories that arrives to a small target, sets the time scale of activation, which in general is much faster than the arrival to the target of only a single trajectory. Analytical ... More
Dissipative particle dynamics simulation of critical pore size in a lipid bilayer membraneOct 18 2017We investigate with computer simulations the critical radius of pores in a lipid bilayer membrane. Ilton et al. (2016) recently showed that nucleated pores in a homopolymer film can increase or decrease in size, depending on whether they are larger or ... More
Active Disassembly and Reassembly of Actin Networks Induces Distinct Biphasic MechanicsOct 10 2017Actin is a key component of the cytoskeleton, which plays central roles in cell motility, division, growth, and tensile strength. To enable this wide range of transient mechanical processes and properties, networks of actin filaments continuously disassemble ... More
Voltage laws for three-dimensional microdomains with cusp-shaped funnels derived from Poisson-Nernst-Planck equationsOct 06 2017We study the electro-diffusion properties of a domain containing a cusp-shaped structure in three dimensions when one ionic specie is dominant. The mathematical problem consists in solving the steady-state Poisson-Nernst-Planck (PNP) equation with an ... More
Particle transport across a channel via an oscillating potentialOct 06 2017Membrane protein transporters alternate their substrate-binding sites between the extracellular and cytosolic side of the membrane according to the alternating access mechanism. Inspired by this intriguing mechanism devised by nature, we study particle ... More
Continuous attractor-based clocks are unreliable phase estimatorsSep 27 2017Statistical estimation theory determines the optimal way of estimating parameters of a fluctuating noisy signal. However, if the estimation is performed on unreliable hardware, a sub-optimal estimation procedure can outperform the previously optimal procedure. ... More
Hydro-osmotic instabilities in active membrane tubesSep 08 2017Jan 30 2018We study a membrane tube with unidirectional ion pumps driving an osmotic pressure difference. A pressure driven peristaltic instability is identified, qualitatively distinct from similar tension-driven Rayleigh type instabilities on membrane tubes. We ... More
Deciphering mRNA Sequence Determinants of Protein Production RateAug 25 2017Mar 08 2018One of the greatest challenges in biophysical models of translation is to identify coding sequences features that affect the rate of translation and therefore the overall protein production in the cell. We propose an analytic method to solve a translation ... More
Active and Passive Transport of Cargo in a Corrugated Channel: A Lattice Model StudyJul 26 2017Apr 07 2018Inside cells, cargos such as vesicles and organelles are transported by molecular motors to their correct locations via active motion on cytoskeletal tracks and passive, Brownian diffusion. During the transportation of cargos, motor-cargo complexes (MCC) ... More
Complexity of Model Testing for Dynamical Systems with Toric Steady StatesJul 24 2017Dec 14 2018In this paper we investigate the complexity of model selection and model testing for dynamical systems with toric steady states. Such systems frequently arise in the study of chemical reaction networks. We do this by formulating these tasks as a constrained ... More
Mesoscopic Modeling of Random Walk and Reactions in Crowded MediaJul 19 2017Mar 01 2018We develop a mesoscopic modeling framework for diffusion in a crowded environment, particularly targeting applications in the modeling of living cells. Through homogenization techniques we effectively coarse-grain a detailed microscopic description into ... More
Encounter time of two loci governed by polymer de-condensation and local chromatin interactionJul 10 2017The time for a DNA sequence to find its homologous depends on a long random search process inside the cell nucleus. Using polymer models, we model and compute here the mean first encounter time (MFET) between two sites located on two different polymer ... More
Why enveloped viruses need cores -- the contribution of a nucleocapsid core to viral buddingJun 15 2017Jul 25 2017During the alphavirus lifecycle, a nucleocapsid core buds through the cell membrane to acquire an outer envelope of lipid membrane and viral glycoproteins. However, the presence of a nucleocapsid core is not required for assembly of infectious particles. ... More