Shaping up synthetic cells.

abstract：:Neuronal cells change their growth properties in response to external physical stimuli such as variations in external temperature, stiffness of the growth substrate, or topographical guidance cues. Detailed knowledge of the mechanisms that control these biomechanical responses is necessary for understanding the basic ...

journal_title：Physical biology

authors： Spedden E,Kaplan DL,Staii C

更新日期：2013-10-01 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：: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：:We propose a three-dimensional mechanical model of embryonic tissue dynamics. Mechanically coupled adherent cells are represented as particles interconnected with elastic beams which can exert non-central forces and torques. Tissue plasticity is modeled by a stochastic process consisting of a connectivity change (addi...

journal_title：Physical biology

authors： Czirok A,Isai DG

更新日期：2014-12-15 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

authors： Dekel E,Mangan S,Alon U

更新日期：2005-06-01 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：:Cells respond to the environment by regulating the expression of genes according to environmental signals. The relation between the input signal level and the expression of the gene is called the gene regulation function. It is of interest to understand the shape of a gene regulation function in terms of the environme...

journal_title：Physical biology

authors： Kalisky T,Dekel E,Alon U

更新日期：2007-11-07 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：:When motile cells come into contact with one another their motion is often considerably altered. In a process termed contact inhibition of locomotion (CIL) cells reshape and redirect their movement as a result of cell-cell contact. Here we describe a mathematical model that demonstrates that CIL alone is sufficient to...

journal_title：Physical biology

authors： Coburn L,Cerone L,Torney C,Couzin ID,Neufeld Z

更新日期：2013-08-01 00:00:00

abstract：:The morphological symmetry of the division process of Escherichia coli is well-known. Recent studies verified that, in optimal growth conditions, most divisions are symmetric, although there are exceptions. We investigate whether such morphological asymmetries in division introduce functional asymmetries between siste...

journal_title：Physical biology

authors： Gupta A,Lloyd-Price J,Oliveira SM,Yli-Harja O,Muthukrishnan AB,Ribeiro AS

更新日期：2014-11-10 00:00:00

abstract：:The detection of gravity plays a fundamental role during the growth and evolution of plants. Although progress has been made in our understanding of the molecular, cellular and physical mechanisms involved in the gravity detection, a coherent scenario consistent with all the observations is still lacking. In this spec...

journal_title：Physical biology

authors： Pouliquen O,Forterre Y,Bérut A,Chauvet H,Bizet F,Legué V,Moulia B

更新日期：2017-05-23 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：: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

authors： Fang X,Wang J

更新日期：2017-02-16 00:00:00

abstract：:Engineering artificial cells to mimic one or multiple fundamental cell biological functions is an emerging area of synthetic biology. Reconstituting functional modules from biological components in vitro is a challenging yet an important essence of bottom-up synthetic biology. Here we describe the concept of building ...

journal_title：Physical biology

authors： Majumder S,Liu AP

更新日期：2017-12-06 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：: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

authors： Nadkarni S,Jung P

更新日期：2004-06-01 00:00:00

abstract：:Mucociliary clearance and cough are the two main natural mucus draining methods in the bronchial tree. If they are affected by a pathology, they can become insufficient or even ineffective, then therapeutic draining of mucus plays a critical role to keep mucus levels in the lungs acceptable. The manipulations of physi...

journal_title：Physical biology

authors： Mauroy B,Fausser C,Pelca D,Merckx J,Flaud P

更新日期：2011-10-01 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：: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：:'ENVIRONMENT' is a computational platform that has been developed in the last few years with the aim to simulate stochastically the dynamics and stability of chemically reacting protocellular systems. Here we present and describe some of its main features, showing how the stochastic kinetics approach can be applied to...

journal_title：Physical biology

authors： Mavelli F,Ruiz-Mirazo K

更新日期：2010-08-11 00:00:00

abstract：:Cells can often choose among several stably heritable phenotypes. Examples are the expressions of genes in eukaryotic cells where long chromosomal regions can adopt persistent and heritable silenced or active states that may be associated with positive feedback in dynamic modification of nucleosomes. We generalize thi...

journal_title：Physical biology

authors： Micheelsen MA,Mitarai N,Sneppen K,Dodd IB

更新日期：2010-06-04 00:00:00

abstract：:How cell collectives move and deposit subunits within a developing embryo is a question of outstanding interest. In many cases, a chemotactic mechanism is employed, where cells move up or down a previously generated attractive or repulsive gradient of signalling molecules. Recent studies revealed the existence of syst...

journal_title：Physical biology

authors： Streichan SJ,Valentin G,Gilmour D,Hufnagel L

更新日期：2011-08-01 00:00:00

abstract：:Cells often have tens of thousands of receptors, even though only a few activated receptors can trigger full cellular responses. Reasons for the overabundance of receptors remain unclear. We suggest that, under certain conditions, the large number of receptors can result in a competition among receptors to be the firs...

journal_title：Physical biology

authors： Cheng X,Merchan L,Tchernookov M,Nemenman I

更新日期：2013-06-01 00:00:00

abstract：:The spatial patterning of three cell fates in a row of competent cells is exemplified by vulva development in the nematode Caenorhabditis elegans. The intercellular signaling network that underlies fate specification is well understood, yet quantitative aspects remain to be elucidated. Quantitative models of the netwo...

journal_title：Physical biology

authors： Félix MA

更新日期：2012-08-01 00:00:00

abstract：:Motile biological cells in tissue often display the phenomenon of durotaxis, i.e. they tend to move towards stiffer parts of substrate tissue. The mechanism for this behavior is not completely understood. We consider simplified models for durotaxis based on the classic persistent random walker scheme. We show that eve...

journal_title：Physical biology

authors： Doering CR,Mao X,Sander LM

更新日期：2018-09-11 00:00:00

abstract：:Traditional experimental biology has provided a mechanistic understanding of cancer in which the malignancy develops through the acquisition of mutations that disrupt cellular processes. Several drugs developed to target such mutations have now demonstrated clinical value. These advances are unequivocal testaments to ...

journal_title：Physical biology

authors： Stites EC

更新日期：2013-04-01 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：:In addition to serving as structural elements and as tracks for motor proteins, microtubules use chemical energy derived from the hydrolysis of GTP to generate forces when growing and shrinking. These forces are used to push or pull on organelles such as chromosomes and the mitotic spindle. If an array of microtubules...

journal_title：Physical biology

authors： Howard J

更新日期：2006-02-28 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：:Type I collagen is a versatile biomaterial that is widely used in medical applications due to its weak antigenicity, robust biocompatibility, and its ability to be modified for a wide array of applications. As such, collagen has become a major component of many tissue engineering scaffolds, drug delivery platforms, an...

journal_title：Physical biology

authors： Hapach LA,VanderBurgh JA,Miller JP,Reinhart-King CA

更新日期：2015-12-21 00:00:00