Theory for the stability and regulation of epigenetic landscapes.

abstract：:The tripartite synapse denotes the junction of a pre- and postsynaptic neuron modulated by a synaptic astrocyte. Enhanced transmission probability and frequency of the postsynaptic current-events are among the significant effects of the astrocyte on the synapse as experimentally characterized by several groups. In thi...

journal_title：Physical biology

authors： Nadkarni S,Jung P

更新日期：2007-01-09 00:00:00

abstract：:How interactions between mechanics and biochemistry lead to the emergence of complex cell and tissue organization is an old question that has recently attracted renewed interest from biologists, physicists, mathematicians and computer scientists. Rapid advances in optical physics, microscopy and computational image an...

journal_title：Physical biology

authors： Lenne PF,Munro E,Heemskerk I,Warmflash A,Bocanegra-Moreno L,Kishi K,Kicheva A,Long Y,Fruleux A,Boudaoud A,Saunders TE,Caldarelli P,Michaut A,Gros J,Maroudas-Sacks Y,Keren K,Hannezo E,Gartner ZJ,Stormo BS,Gladfelter

更新日期：2020-12-04 00:00:00

abstract：:When the author arrived in Berkeley, in the mid 1970s, to study Biophysics he soon felt as if he was engaging himself in a somewhat marginal activity. Biology was then entering another of its cyclical periods of annotation that was to culminate with the human genome project. Two decades later, however, at the end of t...

journal_title：Physical biology

authors： Bustamante CJ

更新日期：2014-10-08 00:00:00

abstract：:Recently, major progress has been made to develop computational models to predict and explain the mechanisms and behaviors of gene regulation. Here, we review progress on how these mechanisms and behaviors have been interpreted with analog models, where cell properties continuously modulate transcription, and digital ...

journal_title：Physical biology

authors： Munsky B,Neuert G

更新日期：2015-06-18 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：: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：:Intermolecular interactions became an inherent part of the structure-function paradigm. Therefore, the generalized concept of protein stability and interactions should consider the balance of stabilizing forces working in different types of intermolecular interactions. We consider here two 'extremes' of protein intera...

journal_title：Physical biology

authors： Berezovsky IN

更新日期：2011-06-01 00:00:00

abstract：:The detection of gravity plays a fundamental role during the growth and evolution of plants. Although progress has been made in our understanding of the molecular, cellular and physical mechanisms involved in the gravity detection, a coherent scenario consistent with all the observations is still lacking. In this spec...

journal_title：Physical biology

authors： Pouliquen O,Forterre Y,Bérut A,Chauvet H,Bizet F,Legué V,Moulia B

更新日期：2017-05-23 00:00:00

abstract：:Efficient nucleotide import is critical to fuel the reverse DNA synthesis that takes place within the HIV-1 capsid. However, the mechanism by which the HIV-1 capsid imports nucleotides is presently unclear. In this work, we carry out a series of Brownian diffusion simulations to elucidate the nucleotide import process...

journal_title：Physical biology

authors： Song G

更新日期：2020-10-07 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 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：: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：: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：: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

abstract：:Transendothelial migration is a crucial process of the metastatic cascade in which a malignant cell attaches itself to the endothelial layer forming the inner wall of a blood or lymph vessel and creates a gap through which it enters into the bloodstream (or lymphatic system) and then is transported to distant parts of...

journal_title：Physical biology

authors： Ramis-Conde I,Chaplain MA,Anderson AR,Drasdo D

更新日期：2009-03-25 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：: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：: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：:Traditionally animal groups have been characterized by the macroscopic patterns that they form. It is now recognised that such patterns convey limited information about the nature of the aggregation as a whole. Aggregate properties cannot be determined by passive observations alone; instead one must interact with them...

journal_title：Physical biology

authors： Reynolds AM

更新日期：2019-04-23 00:00:00

abstract：:Gene-regulation networks contain recurring elementary circuits termed network motifs. It is of interest to understand under which environmental conditions each motif might be selected. To address this, we study one of the most significant network motifs, a three-gene circuit called the coherent feed-forward loop (FFL)...

journal_title：Physical biology

authors： Dekel E,Mangan S,Alon U

更新日期：2005-06-01 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：: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：: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：: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：: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：: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：: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：:A two-dimensional model is proposed for intercellular calcium (Ca(2 +)) waves with Ca(2 +)-induced IP(3) regeneration and the diffusion of IP(3) through gap junctions. Many experimental observations in glial cells, i.e. responding to local mechanical stimulation, glutamate application, mechanical stimulation followed ...

journal_title：Physical biology

authors： Wei F,Shuai J

更新日期：2011-04-01 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