Toward the modeling of mucus draining from the human lung: role of the geometry of the airway tree.

abstract：:A vast literature has explored the genetic interactions among the cellular components regulating gene expression in many organisms. Early on, in the absence of any biochemical definition, regulatory modules were conceived using the strict formalism of genetics to designate the modifiers of phenotype as either cis- or ...

journal_title：Physical biology

authors： Levens D,Benham CJ

更新日期：2011-06-01 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：: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：: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：: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：: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：:Directed cell migration often involves at least two types of cell motility that include multicellular streaming and chain migration. However, what is unclear is how cell contact dynamics and the distinct microenvironments through which cells travel influence the selection of one migratory mode or the other. The embryo...

journal_title：Physical biology

authors： Wynn ML,Rupp P,Trainor PA,Schnell S,Kulesa PM

更新日期：2013-06-01 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：: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：: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 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：: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：: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：: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：: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：:This paper considers the generation of trajectories to a given protein conformation and presents a novel approach based on artificial potential functions--originally proposed for multi-robot navigation. The artificial potential function corresponds to a simplified energy model, but with the novelty that--motivated by ...

journal_title：Physical biology

authors： Ulutaş B,Haliloglu T,Bozma I

更新日期：2009-05-14 00:00:00

abstract：:To address the issue of extracting useful information from large data-set of large scale networks of neurons, we propose an algorithm that involves both algebraic-statistical and topological tools. We investigate the electrical behavior of in vitro cortical assemblies both during spontaneous and stimulus-evoked activi...

journal_title：Physical biology

authors： Pirino V,Riccomagno E,Martinoia S,Massobrio P

更新日期：2015-01-05 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：: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：: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：: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：: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：: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：: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：: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：: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：:In Parkinson's disease (PD), there is evidence that alpha-synuclein (alphaSN) aggregation is coupled to dysfunctional or overburdened protein quality control systems, in particular the ubiquitin-proteasome system. Here, we develop a simple dynamical model for the on-going conflict between alphaSN aggregation and the m...

journal_title：Physical biology

authors： Sneppen K,Lizana L,Jensen MH,Pigolotti S,Otzen D

更新日期：2009-05-01 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：:The single-molecule fluorescence technique is becoming a general and mature tool to probe interactions and dynamics of biomolecules with ultra high precision and accuracy. However, nonspecific adsorption of biomolecules to the flow cells remains a major experimental riddle for the study of many complex biological syst...

journal_title：Physical biology

authors： Pan H,Xia Y,Qin M,Cao Y,Wang W

更新日期：2015-06-29 00:00:00