Near-criticality underlies the behavior of early tumor growth.

abstract：:A two-dimensional model is proposed for intercellular calcium (Ca(2 +)) waves with Ca(2 +)-induced IP(3) regeneration and the diffusion of IP(3) through gap junctions. Many experimental observations in glial cells, i.e. responding to local mechanical stimulation, glutamate application, mechanical stimulation followed ...

journal_title：Physical biology

authors： Wei F,Shuai J

更新日期：2011-04-01 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

authors： Tarle V,Gauquelin E,Vedula SRK,D'Alessandro J,Lim CT,Ladoux B,Gov NS

更新日期：2017-05-03 00:00:00

abstract：:We study the applicability of Van Kampen's linear noise approximation to the calculation of fluctuations in cells due to small number of molecules for simple genetic systems not previously considered. These systems include dimer formation and feedback. We explain why the linear noise approximation can be surprisingly ...

journal_title：Physical biology

authors： Hayot F,Jayaprakash C

更新日期：2004-12-01 00:00:00

abstract：:Branching morphogenesis is a widely spread phenomenon in nature. In organogenesis, it results from the inhomogeneous growth of the epithelial sheet, leading to its repeated branching into surrounding mesoderm. Lung morphogenesis is an emblematic example of tree-like organogenesis common to most mammals. The core signa...

journal_title：Physical biology

authors： Clément R,Douady S,Mauroy B

更新日期：2012-12-01 00:00:00

abstract：:Folate deficiency is accompanied by a decline in the cognitive neurotransmitter acetylcholine and a decline in cognitive performance in mice lacking apolipoprotein E (ApoE-/- mice), a low-density lipoprotein that regulates aspects of lipid metabolism. One direct consequence of folate deficiency is a decline in S-adeno...

journal_title：Physical biology

authors： Serra M,Chan A,Dubey M,Gilman V,Shea TB

更新日期：2008-12-19 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

authors： Deneke C,Lipowsky R,Valleriani A

更新日期：2013-08-01 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

authors： Rochman ND,Popescu DM,Sun SX

更新日期：2018-03-14 00:00:00

abstract：:A series of simulations aimed at elucidating the self-assembly dynamics of spherical virus capsids is described. This little-understood phenomenon is a fascinating example of the complex processes that occur in the simplest of organisms. The fact that different viruses adopt similar structural forms is an indication o...

journal_title：Physical biology

authors： Rapaport DC

更新日期：2010-12-09 00:00:00

abstract：:Tumor metastasis involves a progressive loss of tissue architecture and dissolution of structural boundaries between the epithelium and connective tissue. The basement membrane (BM), a specialized network of extracellular matrix proteins forms a barrier that physically restricts pre-invasive lesions such that they rem...

journal_title：Physical biology

authors： Tanner K

更新日期：2012-12-01 00:00:00

abstract：:Bistable regulatory elements enhance heterogeneity in cell populations and, in multicellular organisms, allow cells to specialize and specify their fate. Our study demonstrates that in a system of bistable genetic switch, the noise characteristics control in which of the two epigenetic attractors the cell population w...

journal_title：Physical biology

authors： Jaruszewicz J,Lipniacki T

更新日期：2013-06-01 00:00:00

abstract：:We report self-consistent Brownian dynamics simulations of a simple electrostatic model of the selectivity filters (SF) of calcium ion channels. They reveal regular structure in the conductance and selectivity as functions of the fixed negative charge Qf at the SF. With increasing Qf, there are distinct regions of hig...

journal_title：Physical biology

authors： Kaufman I,Luchinsky DG,Tindjong R,McClintock PV,Eisenberg RS

更新日期：2013-04-01 00:00:00

abstract：:We study diffusion of macromolecules in a crowded cytoplasm-like environment, focusing on its dependence on composition and its crossover to the anomalous subdiffusion. The crossover and the diffusion itself depend on both the volume fraction and the relative concentration of macromolecules. In accordance with previou...

journal_title：Physical biology

authors： Kondrat S,Zimmermann O,Wiechert W,von Lieres E

更新日期：2015-05-28 00:00:00

abstract：:A cluster of neural crest cells (NCCs) may chemotax up a shallow external gradient to which a single cell is unresponsive. To explain this intriguing 'group advantage', we propose a chemo-mechanical model based on the signaling proteins Rac1 and RhoA. We represent each cell as a polygon with nodes connected by elastic...

journal_title：Physical biology

authors： Merchant B,Feng JJ

更新日期：2020-03-10 00:00:00

abstract：:Cancer cells are known to modify their micro-environment such that it can sustain a larger population, or, in ecological terms, they construct a niche which increases the carrying capacity of the population. It has however been argued that niche construction, which benefits all cells in the tumour, would be selected a...

journal_title：Physical biology

authors： Gerlee P,Anderson AR

更新日期：2015-08-12 00:00:00

abstract：:We present a new particle tracking software algorithm designed to accurately track the motion of low-contrast particles against a background with large variations in light levels. The method is based on a polynomial fit of the intensity around each feature point, weighted by a Gaussian function of the distance from th...

journal_title：Physical biology

authors： Rogers SS,Waigh TA,Zhao X,Lu JR

更新日期：2007-10-09 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

authors： Cao XQ,Zeng J,Yan H

更新日期：2008-09-29 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

authors： Berezovsky IN

更新日期：2011-06-01 00:00:00

abstract：:Single-molecule manipulation has allowed the forced unfolding of multidomain proteins. Here we develop a theory that not only explains these experiments, but also points out a number of difficulties in their interpretation and makes suggestions for further experiments. Our theory is valid for essentially any molecule ...

journal_title：Physical biology

authors： Staple DB,Payne SH,Reddin AL,Kreuzer HJ

更新日期：2009-07-01 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

authors： Li L,Cox EC,Flyvbjerg H

更新日期：2011-08-01 00:00:00

abstract：:The translocation of molecules across cellular membranes or through synthetic nanopores is strongly affected by thermal fluctuations. In this work we study how the dynamics of a polymer in a noisy environment changes when the translocation process is driven by an oscillating electric field. An improved version of the ...

journal_title：Physical biology

authors： Pizzolato N,Fiasconaro A,Adorno DP,Spagnolo B

更新日期：2010-08-04 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

authors： Shi X,You L,Luo RY

更新日期：2019-09-18 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

authors： Krishna S,Semsey S,Jensen MH

更新日期：2009-05-21 00:00:00

abstract：:We propose a reaction model for the palytoxin-sodium-potassium (PTX-Na(+)/K(+)) pump complex. The model, which is similar to the Albers-Post model for Na(+)/K(+)-ATPase, is used to elucidate the effect of PTX on Na(+)/K(+)-ATPase during the enzyme interactions with Na(+) and/or K(+) ions. Conformational substates and ...

journal_title：Physical biology

authors： Rodrigues AM,Almeida AC,Infantosi AF

更新日期：2008-07-29 00:00:00

abstract：:How interactions between mechanics and biochemistry lead to the emergence of complex cell and tissue organization is an old question that has recently attracted renewed interest from biologists, physicists, mathematicians and computer scientists. Rapid advances in optical physics, microscopy and computational image an...

journal_title：Physical biology

authors： Lenne PF,Munro E,Heemskerk I,Warmflash A,Bocanegra-Moreno L,Kishi K,Kicheva A,Long Y,Fruleux A,Boudaoud A,Saunders TE,Caldarelli P,Michaut A,Gros J,Maroudas-Sacks Y,Keren K,Hannezo E,Gartner ZJ,Stormo BS,Gladfelter

更新日期：2020-12-04 00:00:00

abstract：:The maintenance of tissue integrity is essential for the life of multicellular organisms. Healing of a skin wound is a paradigm for how various cell types localize and repair tissue perturbations in an orchestrated fashion. To investigate biophysical mechanisms associated with wound localization, we focus on a model s...

journal_title：Physical biology

authors： Lembong J,Sabass B,Stone HA

更新日期：2017-06-28 00:00:00

abstract：:Voltage-dependent ion channels determine the electric properties of axonal cell membranes. They not only allow the passage of ions through the cell membrane, but also contribute to an additional charging of the cell membrane resulting in the so-called capacitance loading. The switching of the channel gates between an ...

journal_title：Physical biology

authors： Schmid G,Goychuk I,Hänggi P

更新日期：2006-11-22 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

authors： Dunn WB

更新日期：2008-02-20 00:00:00

abstract：:In Parkinson's disease (PD), there is evidence that alpha-synuclein (alphaSN) aggregation is coupled to dysfunctional or overburdened protein quality control systems, in particular the ubiquitin-proteasome system. Here, we develop a simple dynamical model for the on-going conflict between alphaSN aggregation and the m...

journal_title：Physical biology

authors： Sneppen K,Lizana L,Jensen MH,Pigolotti S,Otzen D

更新日期：2009-05-01 00:00:00

abstract：:Modeling the spatiotemporal dynamics of biochemical reaction systems at single-molecule resolution has become feasible with the increase of computing power and is applied especially to cellular signal transduction. For an association reaction the two molecules have to be in contact. Hence, a physically faithful model ...

journal_title：Physical biology

authors： Klann M,Koeppl H

更新日期：2013-08-01 00:00:00

abstract：:Particle tracking offers significant insight into the molecular mechanics that govern the behavior of living cells. The analysis of molecular trajectories that transition between different motive states, such as diffusive, driven and tethered modes, is of considerable importance, with even single trajectories containi...

journal_title：Physical biology

authors： Young DC,Scrimgeour J

更新日期：2018-07-06 00:00:00