Abstract:
:In the intracellular environment, the intrinsic dynamics of microtubule filaments is often hindered by the presence of barriers of various kind, such as kinetochore complexes and cell cortex, which impact their polymerisation force and dynamical properties such as catastrophe rate. We present a theoretical study of the effect of a forced barrier, also subjected to thermal noise, on the statistics of catastrophe events in a single microtubule as well as a "bundle" of two parallel microtubules. For microtubule dynamics, which includes growth, hydrolysis and the consequent dynamic instability, we employ a one-dimensional discrete stochastic model. The dynamics of the barrier is captured by over-damped Langevin equation, while its interaction with a growing filament is assumed to be hard-core repulsion. A unified treatment of the continuum dynamics of the barrier and the discrete dynamics of the filament is realised using a hybrid Fokker-Planck equation. An explicit mathematical formula for the force-dependent catastrophe rate of a single microtubule is obtained by solving the above equation, with minimal assumptions. The prediction agrees well with results of numerical simulations. To investigate the extent of "load-sharing" in a microtubule bundle, and its impact on the frequency of catastrophes, a two-filament model is studied. While equations for the two-filament model predicts equal sharing of load between the filaments, under a mean-field assumption, numerical simulations indicate the existence of a range of load-sharing behaviours, which is characterised using a dimensionless parameter.
journal_name
Phys Bioljournal_title
Physical biologyauthors
Yadav V,Srinivas B,Gopalakrishnan Mdoi
10.1088/1478-3975/abc057subject
Has Abstractpub_date
2020-10-12 00:00:00eissn
1478-3967issn
1478-3975pub_type
杂志文章相关文献
PHYSICAL BIOLOGY文献大全abstract::Traditionally animal groups have been characterized by the macroscopic patterns that they form. It is now recognised that such patterns convey limited information about the nature of the aggregation as a whole. Aggregate properties cannot be determined by passive observations alone; instead one must interact with them...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/ab12b9
更新日期:2019-04-23 00:00:00
abstract::This paper considers the generation of trajectories to a given protein conformation and presents a novel approach based on artificial potential functions--originally proposed for multi-robot navigation. The artificial potential function corresponds to a simplified energy model, but with the novelty that--motivated by ...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/6/3/036008
更新日期:2009-05-14 00:00:00
abstract::Based on the experimental evidence that translating ribosomes stabilize the mRNAs, we introduce and study a theoretical model for the dynamic shielding of mRNA by ribosomes. We present an improved fitting of published decay assay data in E. coli and show that only one third of the decay patterns are exponential. Our n...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/10/4/046008
更新日期:2013-08-01 00:00:00
abstract::We investigate a novel approach for studying protein folding that has evolved from robotics motion planning techniques called probabilistic roadmap methods (PRMs). Our focus is to study issues related to the folding process, such as the formation of secondary and tertiary structures, assuming we know the native fold. ...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/2/4/S09
更新日期:2005-11-09 00:00:00
abstract::We analyze theoretically the effects of excluded-volume interactions between motors on the dynamics of a cargo driven by multiple motors. The model considered shares much in common with others recently proposed in the literature, with the addition of direct interaction between motors and motor back steps. The cargo is...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/7/4/046009
更新日期:2010-11-22 00:00:00
abstract::The functional levels of biological cells or organisms can be separated into the genome, transcriptome, proteome and metabolome. Of these the metabolome offers specific advantages to the investigation of the phenotype of biological systems. The investigation of the metabolome (metabolomics) has only recently appeared ...
journal_title:Physical biology
pub_type: 杂志文章,评审
doi:10.1088/1478-3975/5/1/011001
更新日期:2008-02-20 00:00:00
abstract::Nucleosomes, which contain DNA and proteins, are the basic unit of eukaryotic chromatins. Polymers such as DNA and proteins are dynamic, and their conformational changes can lead to functional changes. Periodic dinucleotide patterns exist in nucleosomal DNA chains and play an important role in the nucleosome structure...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/8/6/066004
更新日期:2011-12-01 00:00:00
abstract::Based on recent experimental data, we design a model for neuronal membrane potentials that incorporates the influence of the surrounding glia (dressed neurons). A neurotransmitter released into the synaptic cleft triggers a Ca(2+) response in nearby glial cells that spreads as a Ca(2+) wave and interacts with other sy...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3967/1/1/004
更新日期:2004-06-01 00:00:00
abstract::The controlling factors that underlie the growth of tumors have often been hard to identify because of the presence in this system of a large number of intracellular biochemical parameters. Here, we propose a simplifying framework to identify the key physical parameters that govern the early growth of tumors. We model...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/13/2/026005
更新日期:2016-04-04 00:00:00
abstract::Epigenetic mechanisms of silencing via heritable chromatin modifications play a major role in gene regulation and cell fate specification. We consider a model of epigenetic chromatin silencing in budding yeast and study the bifurcation diagram and characterize the bistable and the monostable regimes. The main focus of...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/10/3/036005
更新日期:2013-06-01 00:00:00
abstract::Bidirectional cargo transport by molecular motors in cells is a complex phenomenon in which the cargo (usually a vesicle) alternately moves in retrograde and anterograde directions. In this case, teams of oppositely pulling motors (e.g., kinesin and dynein) bind to the cargo, simultaneously, and 'coordinate' their act...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/9/4/046003
更新日期:2012-08-01 00:00:00
abstract::The field of tissue engineering aims to produce living, biological constructs which possess the appropriate spatial ordering of cells and their extra cellular matrix products. The complexity of a single cell and its interactions in a large collective have made development of useful models to assist in tissue culture d...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/5/1/016007
更新日期:2008-04-01 00:00:00
abstract::The single-molecule fluorescence technique is becoming a general and mature tool to probe interactions and dynamics of biomolecules with ultra high precision and accuracy. However, nonspecific adsorption of biomolecules to the flow cells remains a major experimental riddle for the study of many complex biological syst...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/12/4/045006
更新日期:2015-06-29 00:00:00
abstract::Many single-cell observables are highly heterogeneous. A part of this heterogeneity stems from age-related phenomena: the fact that there is a nonuniform distribution of cells with different ages. This has led to a renewed interest in analytic methodologies including use of the 'von Foerster equation' for predicting p...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/aab0e6
更新日期:2018-03-14 00:00:00
abstract::The DFT:B3LYP (6-31G** basis set) method, including the hyperfine and spin-orbit couplings (HFC and SOC, respectively), is used to study the separation of two complementary trinucleotide sequences, (dC-dG-dA)-(dG-dC-dT), upon the action of two Mg(2+) cofactors (a simplified model). The computations reveal a crossing o...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/12/6/066017
更新日期:2015-12-10 00:00:00
abstract::Oscillations play an important physiological role in a variety of biological systems. For example, respiration and carbohydrate synthesis are coupled to the circadian clock in cyanobacteria (Ishiura et al 1998 Science 281 1519) and ultradian oscillations with time periods of a few hours have been observed in immune re...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/6/3/036009
更新日期:2009-05-21 00:00:00
abstract::Circular DNA in viruses and bacteria is often knotted. While mathematically problematic, the determination of the knot size is crucial for the study of the physical and biological behaviour of long macromolecules. Here, we review work on the size distribution of these knots under equilibrium conditions. We discuss kno...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/6/2/025012
更新日期:2009-07-01 00:00:00
abstract::A vast literature has explored the genetic interactions among the cellular components regulating gene expression in many organisms. Early on, in the absence of any biochemical definition, regulatory modules were conceived using the strict formalism of genetics to designate the modifiers of phenotype as either cis- or ...
journal_title:Physical biology
pub_type: 杂志文章,评审
doi:10.1088/1478-3975/8/3/035011
更新日期:2011-06-01 00:00:00
abstract::Thrombosis accounts for 80% of deaths in patients with diabetes mellitus. Diabetic patients demonstrate tortuous microvessels and larger than normal platelets. Large platelets are associated with increased platelet activation and thrombosis, but the physical effects of large platelets in the microscale processes of th...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/10/5/056003
更新日期:2013-10-01 00:00:00
abstract::Intermolecular interactions became an inherent part of the structure-function paradigm. Therefore, the generalized concept of protein stability and interactions should consider the balance of stabilizing forces working in different types of intermolecular interactions. We consider here two 'extremes' of protein intera...
journal_title:Physical biology
pub_type: 杂志文章,评审
doi:10.1088/1478-3975/8/3/035002
更新日期:2011-06-01 00:00:00
abstract::Directed cell migration often involves at least two types of cell motility that include multicellular streaming and chain migration. However, what is unclear is how cell contact dynamics and the distinct microenvironments through which cells travel influence the selection of one migratory mode or the other. The embryo...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/10/3/035003
更新日期:2013-06-01 00:00:00
abstract::Cellular networks have been the focus of studies in modern systems biology. They are crucial in understanding cell functions and related diseases. We review some past progress in both the theory and experiments, and we also provide several future perspectives for the field. ...
journal_title:Physical biology
pub_type: 杂志文章,评审
doi:10.1088/1478-3975/aa5b6a
更新日期:2017-02-16 00:00:00
abstract::We model the motility of Dictyostelium cells in a systematic data-driven manner. We deduce a minimal dynamical model that reproduces the statistical features of experimental trajectories. These are trajectories of the centroid of the cell perimeter, which is more sensitive to pseudopod activity than the usual tracking...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/8/4/046006
更新日期:2011-08-01 00:00:00
abstract::Monolayer expansion has generated great interest as a model system to study collective cell migration. During such an expansion the culture front often develops 'fingers', which we have recently modeled using a proposed feedback between the curvature of the monolayer's leading edge and the outward motility of the edge...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/aa6591
更新日期:2017-05-03 00:00:00
abstract::How do the cells in our body reconfigure their shape to achieve complex tasks like migration and mitosis, yet maintain their shape in response to forces exerted by, for instance, blood flow and muscle action? Cell shape control is defined by a delicate mechanical balance between active force generation and passive mat...
journal_title:Physical biology
pub_type: 杂志文章,评审
doi:10.1088/1478-3975/aab923
更新日期:2018-04-30 00:00:00
abstract::Gravity or ultracentrifuge settling of colloidal particles and macromolecules usually involves several disperse species, either because natural and industrial colloids display a large size polydispersity, or because additives are put in on purpose to allow for density-based fractionation of the suspension. Such 'macro...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/10/4/045005
更新日期:2013-08-01 00:00:00
abstract::The glycolytic enzyme pyruvate kinase M2 (PKM2) exists in both catalytically inactive dimeric and active tetrameric forms. In cancer cells, PKM2 dimer predominance contributes to tumor growth by triggering glycolytic reprogramming. However, the mechanism that promotes PKM2 dimer predominance over tetramer in cancer ce...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/ab3f5a
更新日期:2019-09-18 00:00:00
abstract::Gene-regulation networks contain recurring elementary circuits termed network motifs. It is of interest to understand under which environmental conditions each motif might be selected. To address this, we study one of the most significant network motifs, a three-gene circuit called the coherent feed-forward loop (FFL)...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/2/2/001
更新日期:2005-06-01 00:00:00
abstract::Sequence-dependent DNA flexibility is an important structural property originating from the DNA 3D structure. In this paper, we investigate the DNA flexibility of the budding yeast (S. Cerevisiae) replication origins on a genome-wide scale using flexibility parameters from two different models, the trinucleotide and t...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/5/3/036012
更新日期:2008-09-29 00:00:00
abstract::Peptoids of alpha- and beta-peptides (alpha- and beta-peptoids) can be obtained by shifting the amino acid side chains from the backbone carbon atoms of the monomer constituents to the peptide nitrogen atoms. They are, therefore, N-substituted poly-glycines and poly-beta-alanines, respectively. Due to the substituted ...
journal_title:Physical biology
pub_type: 杂志文章,评审
doi:10.1088/1478-3975/3/1/S01
更新日期:2006-02-02 00:00:00