Intercellular calcium waves in glial cells with bistable dynamics.

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：: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：: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：:The important role of cation-chloride co-transporters in epilepsy is being supported by an increasing number of investigations. However, enormous complexity is involved since the action of these co-transporters has effects on the ionic homeostasis influencing directly the neuronal excitability and the tissue propensit...

journal_title：Physical biology

authors： Lopes MR,Santos LE,Rodrigues AM,Duarte MA,Infantosi AF,Scorza FA,Arida RM,Madureira AP,da Silveira GA,dos Santos IC,Cavalheiro EA,de Almeida AC

更新日期：2013-10-01 00:00:00

abstract：:We carry out systematic Monte Carlo simulations of Gō lattice proteins to investigate and compare the folding processes of two model proteins whose native structures differ from each other due to the presence of a trefoil knot located near the terminus of one of the protein chains. We show that the folding time of the...

journal_title：Physical biology

authors： Faísca PF,Travasso RD,Charters T,Nunes A,Cieplak M

更新日期：2010-02-03 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：:Cells moving on a two dimensional substrate generate motion by polymerizing actin filament networks inside a flat membrane protrusion. New filaments are generated by branching off existing ones, giving rise to branched network structures. We investigate the force-extension relation of branched filaments, grafted on an...

journal_title：Physical biology

authors： Razbin M,Falcke M,Benetatos P,Zippelius A

更新日期：2015-06-04 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：: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：:'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：: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：:The asymmetric cell division cycle in Caulobacter crescentus is controlled by an elaborate molecular mechanism governing the production, activation and spatial localization of a host of interacting proteins. In previous work, we proposed a deterministic mathematical model for the spatiotemporal dynamics of six major r...

journal_title：Physical biology

authors： Li F,Subramanian K,Chen M,Tyson JJ,Cao Y

更新日期：2016-06-25 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：: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：: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

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：: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 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：: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：: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：:Lipid molecules, structural components of biomembranes, have been proposed for an important role in membrane fusion. Through various techniques based on a protein-reconstituted vesicle-vesicle fusion system, we investigated the influence of several lipid molecules on different stages of a yeast soluble N-ethylmaleimid...

journal_title：Physical biology

authors： Lai Y,Zhao L,Bu B,Lou X,Li D,Ji B,Liu J,Diao J,Shin YK

更新日期：2015-04-21 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：:Tumors consist of multiple cell sub-populations including cancer stem cells (CSCs), transiently amplifying cells and terminally differentiated cells (TDCs), with the CSC fraction dictating the aggressiveness of the tumor and drug sensitivity. In epithelial cancers, tumor growth is influenced greatly by properties of t...

journal_title：Physical biology

authors： Kumar S,Kulkarni R,Sen S

更新日期：2016-04-29 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

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：: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：:Successful biological development via spatial regulation of cell differentiation relies on the action of multiple signaling molecules that are known as morphogens. It is now well-established that signaling molecules create non-uniform concentration profiles, morphogen gradients, that activate different genes, leading ...

journal_title：Physical biology

authors： Teimouri H,Kolomeisky AB

更新日期：2015-04-17 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：: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