Modeling proteasome dynamics in Parkinson's disease.

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：: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：: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：: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：: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：: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：: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：:Bidirectional cargo transport by molecular motors in cells is a complex phenomenon in which the cargo (usually a vesicle) alternately moves in retrograde and anterograde directions. In this case, teams of oppositely pulling motors (e.g., kinesin and dynein) bind to the cargo, simultaneously, and 'coordinate' their act...

journal_title：Physical biology

authors： Bhat D,Gopalakrishnan M

更新日期：2012-08-01 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：: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：:The mechanical behavior of living murine T-lymphocytes was assessed by atomic force microscopy (AFM). A robust experimental procedure was developed to overcome some features of lymphocytes, in particular their spherical shape and non-adherent character. The procedure included the immobilization of the lymphocytes on a...

journal_title：Physical biology

authors： Daza R,Cruces J,Arroyo-Hernández M,Marí-Buyé N,De la Fuente M,Plaza GR,Elices M,Pérez-Rigueiro J,Guinea GV

更新日期：2015-03-19 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：:The DFT:B3LYP (6-31G** basis set) method, including the hyperfine and spin-orbit couplings (HFC and SOC, respectively), is used to study the separation of two complementary trinucleotide sequences, (dC-dG-dA)-(dG-dC-dT), upon the action of two Mg(2+) cofactors (a simplified model). The computations reveal a crossing o...

journal_title：Physical biology

authors： Tulub AA,Stefanov VE

更新日期：2015-12-10 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：: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 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：:Cell signaling is achieved predominantly by reversible phosphorylation-dephosphorylation reaction cascades. Up until now, circuits conferring adaptation have all required the presence of a cascade with some type of closed topology: negative-feedback loop with a buffering node, or incoherent feed-forward loop with a pr...

journal_title：Physical biology

authors： Srividhya J,Li Y,Pomerening JR

更新日期：2011-08-01 00:00:00

abstract：:A model of ligand-induced intracellular calcium (Ca2+) responses incorporating phospholipase C (PLC) and protein kinase C (PKC) is developed for the purpose of understanding the mechanisms underlying the observed temporal patterns of intracellular calcium (Ca(i)2+) under sustained agonist stimulation. Some studies hav...

journal_title：Physical biology

authors： Kang M,Othmer HG

更新日期：2007-12-13 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：:Cells of the immune system are confronted with opposing pro- and anti-inflammatory signals. Dendritic cells (DC) integrate these cues to make informed decisions whether to initiate an immune response. Confronted with exogenous microbial stimuli, DC endogenously produce both anti- (IL-10) and pro-inflammatory (TNFα) cu...

journal_title：Physical biology

authors： Marcou Q,Carmi-Levy I,Trichot C,Soumelis V,Mora T,Walczak AM

更新日期：2018-05-16 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 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：:Electrostatic interaction is the driving force for the encapsulation by virus coat proteins of nanoparticles such as quantum dots, gold particles and magnetic beads for, e.g., imaging and therapeutic purposes. In recent experimental work, Daniel et al (2010 ACS Nano 4 3853-60) found the encapsulation efficiency to sen...

journal_title：Physical biology

authors： Lin HK,van der Schoot P,Zandi R

更新日期：2012-12-01 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

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：:By combining optical tweezers-assisted dynamic force spectroscopy experiments with fluorescence activated cell sorting (FACS), we demonstrate a new approach to reducing the data variance in measuring receptor-ligand interactions on a single molecule level by ensuring similar coating densities. Therefore, the carboxyfl...

journal_title：Physical biology

authors： Stangner T,Singer D,Wagner C,Gutsche C,Ueberschär O,Hoffmann R,Kremer F

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：: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：: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：: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