Requirements for efficient cell-type proportioning: regulatory timescales, stochasticity and lateral inhibition.

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：:Particle-based simulators represent molecules of interest with point-like particles that diffuse and react in continuous space. These simulators are often used to investigate spatial or stochastic aspects of biochemical systems. This paper presents new particle-based simulation algorithms for modeling interactions bet...

journal_title：Physical biology

authors： Andrews SS

更新日期：2009-11-12 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：: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：:Computer simulations of beta-hairpin folding are relatively difficult, especially those based on the explicit water model. This greatly limits the complete analysis and understanding of their folding mechanisms. In this paper, we use the generalized Born/solvent accessible implicit solvent model to simulate the foldin...

journal_title：Physical biology

authors： Chen C,Xiao Y

更新日期：2006-08-24 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：: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 th...

journal_title：Physical biology

authors： Yadav V,Srinivas B,Gopalakrishnan M

更新日期：2020-10-12 00:00:00

abstract：:The importance of the tumor microenvironment in cancer progression is undisputed, yet the significance of biophysical forces in the microenvironment remains poorly understood. Interstitial fluid flow is a nearly ubiquitous and physiologically relevant biophysical force that is elevated in tumors because of tumor-assoc...

journal_title：Physical biology

authors： Shieh AC,Swartz MA

更新日期：2011-02-01 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

authors： Thomas S,Song G,Amato NM

更新日期：2005-11-09 00:00:00

abstract：:Gene expression is an intrinsically noisy process, typically, producing mRNAs and proteins in bursts. An important description of such stochastic processes can be done in terms of the mean first passage time (MFPT), i.e., the time taken by mRNAs/proteins to reach a particular threshold. We study the role of burstiness...

journal_title：Physical biology

authors： Shreshtha M,Surendran A,Ghosh A

更新日期：2016-05-20 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：: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：:With the development of next-generation sequencing technologies, many large scale experimental efforts aim to map genotypic variability among individuals. This natural variability in populations fuels many fundamental biological processes, ranging from evolutionary adaptation and speciation to the spread of genetic di...

journal_title：Physical biology

authors： Razo-Mejia M,Boedicker JQ,Jones D,DeLuna A,Kinney JB,Phillips R

更新日期：2014-04-01 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 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：:Asexual reproduction in multicellular organisms is a complex biophysical process that is not yet well understood quantitatively. Here, we report a detailed population study for the asexual freshwater planarian Schmidtea mediterranea, which can reproduce via transverse fission due to a large stem cell contingent. Our l...

journal_title：Physical biology

authors： Dunkel J,Talbot J,Schötz EM

更新日期：2011-04-01 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

authors： Cao XQ,Zeng J,Yan H

更新日期：2008-09-29 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 majority of chronic infections are caused by biofilms, which have higher levels of antibiotic resistance than planktonic growth. Violet-blue 405 nm light has recently emerged as a novel bactericide, but limited studies have been conducted on its effectiveness against biofilms. We found that in response to 405 nm l...

journal_title：Physical biology

authors： Blee JA,Roberts IS,Waigh TA

更新日期：2020-03-04 00:00:00

abstract：:Protein-protein interactions are central to biology and, in this 'post-genomic era', prediction of these interactions has become the goal of many computational efforts. Close inspection of even relatively simple biological regulatory circuitry reveals multiple levels of control of the contributing protein interactions...

journal_title：Physical biology

authors： Beckett D

更新日期：2005-06-01 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：:Growing evidence suggests that critical cellular processes are profoundly influenced by the cross talk between extracellular nanomechanical forces and the material properties of the cellular microenvironment. Although many studies have examined either the effect of nanomechanical forces or the material properties of t...

journal_title：Physical biology

authors： Al-Rekabi Z,Pelling AE

更新日期：2013-12-01 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：: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：: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：: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：: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

authors： Baldauf C,Günther R,Hofmann HJ

更新日期：2006-02-02 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：: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

authors： Mulla Y,Aufderhorst-Roberts A,Koenderink GH

更新日期：2018-04-30 00:00:00

abstract：:This paper gives an overview of the coarse-grained models of phospholipids recently developed by the authors in the frame of a hybrid particle-field molecular dynamics technique. This technique employs a special class of coarse-grained models that are gaining popularity because they allow simulations of large scale sy...

journal_title：Physical biology

authors： Milano G,Kawakatsu T,De Nicola A

更新日期：2013-08-01 00:00:00