Frustrated bistability as a means to engineer oscillations in biological systems.

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：:Cancer cells are known to modify their micro-environment such that it can sustain a larger population, or, in ecological terms, they construct a niche which increases the carrying capacity of the population. It has however been argued that niche construction, which benefits all cells in the tumour, would be selected a...

journal_title：Physical biology

authors： Gerlee P,Anderson AR

更新日期：2015-08-12 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：: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：: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：: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 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 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：: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：:The study on aerial plant organs (leaves and stems) motions is reviewed. The history of observations and studies is put in the perspective of the ideas surrounding them, leading to a presentation of the current classification of these motions. After showing the shortcomings of such a classification, we present, follow...

journal_title：Physical biology

authors： Rivière M,Derr J,Douady S

更新日期：2017-08-21 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：: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：: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 Golgi apparatus has intrigued researchers since its discovery and despite the advances, there are still many open questions in regards to its shape and function. We propose a mechanical model of Golgi apparatus stack and explain its most elementary geometrical properties: the equilibrium number of cisternae, the s...

journal_title：Physical biology

authors： Jelerčič U

更新日期：2019-09-05 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：:Based on the experimental evidence that translating ribosomes stabilize the mRNAs, we introduce and study a theoretical model for the dynamic shielding of mRNA by ribosomes. We present an improved fitting of published decay assay data in E. coli and show that only one third of the decay patterns are exponential. Our n...

journal_title：Physical biology

authors： Deneke C,Lipowsky R,Valleriani A

更新日期：2013-08-01 00:00:00

abstract：:Several viruses exploit clathrin-mediated endocytosis to gain entry into host cells. This process is also used extensively in biomedical applications to deliver nanoparticles (NPs) to diseased cells. The internalization of these nano-objects is controlled by the assembly of a clathrin-containing protein coat on the cy...

journal_title：Physical biology

authors： Banerjee A,Berezhkovskii A,Nossal R

更新日期：2016-02-12 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：:A central question in eukaryotic cell biology asks, during cell division, how is the growth and distribution of organelles regulated to ensure each daughter cell receives an appropriate amount. For vacuoles in budding yeast, there are well described organelle-to-cell size scaling trends as well as inheritance mechanis...

journal_title：Physical biology

authors： Chadwick WL,Biswas SK,Bianco S,Chan YM

更新日期：2020-10-09 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：: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

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：: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：:In recent years, by using modern imaging techniques, scientists have found evidence of collaboration between different types of stem cells (SCs), and proposed a bi-compartmental organization of the SC niche. Here we create a class of stochastic models to simulate the dynamics of such a heterogeneous SC niche. We consi...

journal_title：Physical biology

authors： Shahriyari L,Komarova NL

更新日期：2015-07-31 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：: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：: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：:Staphylococcus aureus is an important pathogen, giving rise to antimicrobial resistance in cell strains such as Methicillin Resistant S. aureus (MRSA). Here we report an image analysis framework for automated detection and image segmentation of cells in S. aureus cell clusters, and explicit identification of their cel...

journal_title：Physical biology

authors： Wollman AJ,Miller H,Foster S,Leake MC

更新日期：2016-10-17 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：: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