A stochastic spatiotemporal model of a response-regulator network in the Caulobacter crescentus cell cycle.

abstract：:Circular DNA in viruses and bacteria is often knotted. While mathematically problematic, the determination of the knot size is crucial for the study of the physical and biological behaviour of long macromolecules. Here, we review work on the size distribution of these knots under equilibrium conditions. We discuss kno...

journal_title：Physical biology

authors： Orlandini E,Stella AL,Vanderzande C

更新日期：2009-07-01 00:00:00

abstract：:Thrombosis accounts for 80% of deaths in patients with diabetes mellitus. Diabetic patients demonstrate tortuous microvessels and larger than normal platelets. Large platelets are associated with increased platelet activation and thrombosis, but the physical effects of large platelets in the microscale processes of th...

journal_title：Physical biology

authors： Chesnutt JK,Han HC

更新日期：2013-10-01 00:00:00

abstract：:Self-organization processes in multicellular aggregates of bacteria and amoebae offer fascinating insights into the evolution of cooperation and differentiation of cells. During myxobacterial development a variety of spatio-temporal patterns emerges such as counterpropagating waves of cell density that are known as ri...

journal_title：Physical biology

authors： Börner U,Deutsch A,Bär M

更新日期：2006-06-23 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：: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：: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：: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：: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：: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：: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：: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：: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：: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：: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：:Calcium homeostasis is considered to be one of the most important factors for the contraction and relaxation of the heart muscle. However, under some pathological conditions, such as heart failure (HF), calcium homeostasis is disordered, and spontaneous waves may occur. In this study, we developed a mathematical model...

journal_title：Physical biology

authors： Lu L,Xia L,Ye X,Cheng H

更新日期：2010-05-26 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：: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：: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：: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：: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：: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：: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：:Neurofilaments are transported along axons stochastically in a stop-and-go manner, cycling between brief bouts of rapid movement and pauses that can vary from seconds to hours in length. Presently the only way to analyze neurofilament pausing experimentally on both long and short time scales is the pulse-escape method...

journal_title：Physical biology

authors： Li Y,Brown A,Jung P

更新日期：2014-04-01 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：:The source of increased stability in proteins from organisms that thrive in extreme thermal environments is not well understood. Previous experimental and theoretical studies have suggested many different features possibly responsible for such thermostability. Many of these thermostabilizing mechanisms can be accounte...

journal_title：Physical biology

authors： Rader AJ

更新日期：2009-12-11 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 maintenance of tissue integrity is essential for the life of multicellular organisms. Healing of a skin wound is a paradigm for how various cell types localize and repair tissue perturbations in an orchestrated fashion. To investigate biophysical mechanisms associated with wound localization, we focus on a model s...

journal_title：Physical biology

authors： Lembong J,Sabass B,Stone HA

更新日期：2017-06-28 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