Cost-benefit theory and optimal design of gene regulation functions.

abstract：:Oncolytic virotherapy-the use of viruses that specifically kill tumor cells-is an innovative and highly promising route for treating cancer. However, its therapeutic outcomes are mainly impaired by the host immune response to the viral infection. In this paper, we propose a multiscale mathematical model to study how t...

journal_title：Physical biology

authors： Paiva LR,Silva HS,Ferreira SC,Martins ML

更新日期：2013-04-01 00:00:00

abstract：:Recent advances in clinical medicine have elucidated two significantly different subtypes of glioblastoma which carry very different prognoses, both defined by mutations in isocitrate dehydrogenase-1 (IDH-1). The mechanistic consequences of this mutation have not yet been fully clarified, with conflicting opinions exi...

journal_title：Physical biology

authors： Basanta D,Scott JG,Rockne R,Swanson KR,Anderson AR

更新日期：2011-02-01 00:00:00

abstract：:The Q-cycle mechanism plays an important role in the conversion of the redox energy into the energy of the proton electrochemical gradient across the biomembrane. The bifurcated electron transfer reaction, which is built into this mechanism, recycles one electron, thus allowing us to translocate two protons per one el...

journal_title：Physical biology

authors： Smirnov AY,Nori F

更新日期：2012-02-01 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

authors： Wynn ML,Rupp P,Trainor PA,Schnell S,Kulesa PM

更新日期：2013-06-01 00:00:00

abstract：:Cancer may result from localized failure of instructive cues that normally orchestrate cell behaviors toward the patterning needs of the organism. Steady-state gradients of transmembrane voltage (V(mem)) in non-neural cells are instructive, epigenetic signals that regulate pattern formation during embryogenesis and mo...

journal_title：Physical biology

authors： Lobikin M,Chernet B,Lobo D,Levin M

更新日期：2012-12-01 00:00:00

abstract：:Increasing numbers of physicists engage in research activities that address biological questions from physics perspectives or strive to develop physics insights from active biological processes. The on-going development and success of such activities morph our ways of thinking about what it is to 'do biophysics' and a...

journal_title：Physical biology

authors： Hoogenboom BW,Leake MC

更新日期：2018-07-06 00:00:00

abstract：:The proper functioning of multicellular organisms requires the robust establishment of precise proportions between distinct cell types. This developmental differentiation process typically involves intracellular regulatory and stochastic mechanisms to generate cell-fate diversity as well as intercellular signaling mec...

journal_title：Physical biology

authors： Pfeuty B,Kaneko K

更新日期：2016-05-11 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

authors： Levens D,Benham CJ

更新日期：2011-06-01 00:00:00

abstract：:Epithelial-to-mesenchymal transition (EMT) is a fundamental developmental process wherein polarized epithelial cells lose their junctional architecture and apical-basal polarity to become motile mesenchymal cells, and there is emerging evidence for its role in propagating tumor dissemination. While many multifaceted n...

journal_title：Physical biology

authors： Antony J,Thiery JP,Huang RY

更新日期：2019-05-07 00:00:00

abstract：:The one-cell amphibian embryo is modeled as a rigid spherical shell containing equal volumes of two immiscible fluids with different densities and viscosities and a surface tension between them. The fluids represent denser yolk in the bottom hemisphere and clearer cytoplasm and the germinal vesicle in the top hemisphe...

journal_title：Physical biology

authors： Nouri C,Luppes R,Veldman AE,Tuszynski JA,Gordon R

更新日期：2008-04-10 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

authors： Pietak A,Waldman SD

更新日期：2008-04-01 00:00:00

abstract：:Identifying the cues followed by cells is key to understand processes as embryonic development, tissue homeostasis, or several pathological conditions. Based on a durotaxis model, it is shown that cells moving on predeformed thin elastic membrane follow the direction of increasing strain of the substrate. This mechani...

journal_title：Physical biology

authors： Márquez S,Reig G,Concha M,Soto R

更新日期：2019-09-06 00:00:00

abstract：:Bacteria such as Escherichia coli propel themselves by rotating a bundle of helical filaments, each driven by a rotary motor embedded in the cell membrane. Each filament is an assembly of thousands of copies of the protein flagellin which assumes two different states. We model the filament by an elastic network of rig...

journal_title：Physical biology

authors： Speier C,Vogel R,Stark H

更新日期：2011-08-01 00:00:00

abstract：:In this article the notion of metabolic turnover is revisited in the light of recent results of out-of-equilibrium thermodynamics. By means of Monte Carlo methods we perform an exact sampling of the enzymatic fluxes in a genome scale metabolic network of E. coli in stationary growth conditions from which we infer the ...

journal_title：Physical biology

authors： De Martino D

更新日期：2016-01-29 00:00:00

abstract：:Surface plasmon resonance (SPR) chips are widely used to measure association and dissociation rates for the binding kinetics between two species of chemicals, e.g., cell receptors and ligands. It is commonly assumed that ligands are spatially well mixed in the SPR region, and hence a mean-field rate equation descripti...

journal_title：Physical biology

authors： Carroll J,Raum M,Forsten-Williams K,Täuber UC

更新日期：2016-12-06 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

authors： Ulutaş B,Haliloglu T,Bozma I

更新日期：2009-05-14 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：:Host-to-host variability with respect to interactions between microorganisms and multicellular hosts are commonly observed in infection and in homeostasis. However, the majority of mechanistic models used to analyze host-microorganism relationships, as well as most of the ecological theories proposed to explain coevol...

journal_title：Physical biology

authors： Mukherjee S,Weimer KE,Seok SC,Ray WC,Jayaprakash C,Vieland VJ,Swords WE,Das J

更新日期：2014-12-04 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：: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：:Shelter-in-place and other confinement strategies implemented in the current COVID-19 pandemic have created stratified patterns of contacts between people: close contacts within households and more distant contacts between the households. The epidemic transmission dynamics is significantly modified as a consequence. W...

journal_title：Physical biology

authors： Huber G,Kamb M,Kawagoe K,Li LM,Veytsman B,Yllanes D,Zigmond D

更新日期：2020-10-21 00:00:00

abstract：:Chemotaxis is the process by which cells sense changes in their chemical environment and move towards more favorable conditions. In divergent species of bacteria, the chemotaxis proteins localize to the poles of the cell and information is transferred to the flagellar motors through the phosphorylation of a soluble pr...

journal_title：Physical biology

authors： Rao CV,Kirby JR,Arkin AP

更新日期：2005-07-14 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：: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：: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

authors： Piazza R,Buzzaccaro S,Secchi E,Parola A

更新日期：2013-08-01 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

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：: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：:We present a simple two-state model to understand the size-dependent endocytosis of nanoparticles. Using this model, we elucidate the relevant energy terms required to understand the size-dependent uptake mechanism and verify it by correctly predicting the behavior at large and small particle sizes. In the absence of ...

journal_title：Physical biology

authors： Chaudhuri A,Battaglia G,Golestanian R

更新日期：2011-08-01 00:00:00

abstract：:Efficient nucleotide import is critical to fuel the reverse DNA synthesis that takes place within the HIV-1 capsid. However, the mechanism by which the HIV-1 capsid imports nucleotides is presently unclear. In this work, we carry out a series of Brownian diffusion simulations to elucidate the nucleotide import process...

journal_title：Physical biology

authors： Song G

更新日期：2020-10-07 00:00:00

abstract：:Cell division is accompanied by dramatic changes in shape that ultimately lead to the physical separation of one cell into two. In 2D microenvironments, cells round up and remain adhered onto the substrate by thin retraction fibers during division. In contrast, in 3D environments, cells divide exhibiting long protrusi...

journal_title：Physical biology

authors： Caballero D,Pinto IM,Rubinstein BY,Samitier J

更新日期：2019-10-10 00:00:00