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 of the molecular interaction assumes non-overlapping molecules that interact at their surfaces (boundary scheme). For performance reasons, this model can be replaced by particles that can overlap and react when they are closer than a certain distance with a reaction probability (volume scheme). Here we present an analytical approximation for the reaction probability in the volume scheme and compare the volume- with the boundary scheme. A dissociation reaction, in contrast, creates two molecules next to each other. If the reaction is reversible, these two products can directly re-bind again, leading to an overestimation of the dimerized state in the simulation. We show how the correct recombination rate can be achieved if the products of the dissociation are placed at identical positions, but cannot react for a certain timespan. This refractory time corresponds to the completion of the diffusion-controlled dissociation of the two molecules to their contact distance r(i)+r(j) at t = τ ×(r(i)+r(j))²/(D(i)+D(j) with τ = 1/10 for molecules with radii r(i) and r(j) and diffusion coefficients D(i) and D(j), respectively.
journal_name
Phys Bioljournal_title
Physical biologyauthors
Klann M,Koeppl Hdoi
10.1088/1478-3975/10/4/046005subject
Has Abstractpub_date
2013-08-01 00:00:00pages
046005issue
4eissn
1478-3967issn
1478-3975journal_volume
10pub_type
杂志文章相关文献
PHYSICAL BIOLOGY文献大全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
pub_type: 杂志文章
doi:10.1088/1478-3975/13/6/066010
更新日期:2016-12-06 00:00:00
abstract::Nucleosomes, which contain DNA and proteins, are the basic unit of eukaryotic chromatins. Polymers such as DNA and proteins are dynamic, and their conformational changes can lead to functional changes. Periodic dinucleotide patterns exist in nucleosomal DNA chains and play an important role in the nucleosome structure...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/8/6/066004
更新日期:2011-12-01 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
pub_type: 杂志文章
doi:10.1088/1478-3975/8/5/056006
更新日期:2011-10-01 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
pub_type: 杂志文章
doi:10.1088/1478-3975/2/4/S09
更新日期:2005-11-09 00:00:00
abstract::This special issue consists of 11 original papers that elaborate on work presented at the Fourth Annual q-bio Conference on Cellular Information Processing, which was held on the campus of St John's College in Santa Fe, New Mexico, USA, 11-14 August 2010. Now in its fourth year, the q-bio conference has changed consid...
journal_title:Physical biology
pub_type:
doi:10.1088/1478-3975/8/5/050301
更新日期:2011-10-01 00:00:00
abstract::We carry out systematic Monte Carlo simulations of Gō lattice proteins to investigate and compare the folding processes of two model proteins whose native structures differ from each other due to the presence of a trefoil knot located near the terminus of one of the protein chains. We show that the folding time of the...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/7/1/016009
更新日期:2010-02-03 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
pub_type: 杂志文章
doi:10.1088/1478-3975/aa6b67
更新日期:2017-06-28 00:00:00
abstract::This report presents a simple model that describes the motion of a single Dictyostelium discoideum cell exposed to a traveling wave of cyclic adenosine monophosphate (cAMP). The model incorporates two types of responses to stimulation by cAMP: the changes in the polarity and motility of the cell. The periodic change i...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/12/2/026004
更新日期:2015-03-19 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
pub_type: 杂志文章
doi:10.1088/1478-3975/13/1/016003
更新日期:2016-01-29 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
pub_type: 杂志文章
doi:10.1088/1478-3975/12/2/026005
更新日期:2015-03-19 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
pub_type: 杂志文章
doi:10.1088/1478-3975/12/1/016007
更新日期:2015-01-05 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
pub_type: 杂志文章,评审
doi:10.1088/1478-3975/12/6/061002
更新日期:2015-12-21 00:00:00
abstract::Motile biological cells in tissue often display the phenomenon of durotaxis, i.e. they tend to move towards stiffer parts of substrate tissue. The mechanism for this behavior is not completely understood. We consider simplified models for durotaxis based on the classic persistent random walker scheme. We show that eve...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/aadc37
更新日期:2018-09-11 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
pub_type: 杂志文章
doi:10.1088/1478-3975/ab759a
更新日期:2020-03-04 00:00:00
abstract::We study the applicability of Van Kampen's linear noise approximation to the calculation of fluctuations in cells due to small number of molecules for simple genetic systems not previously considered. These systems include dimer formation and feedback. We explain why the linear noise approximation can be surprisingly ...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3967/1/4/002
更新日期:2004-12-01 00:00:00
abstract::The spatial patterning of three cell fates in a row of competent cells is exemplified by vulva development in the nematode Caenorhabditis elegans. The intercellular signaling network that underlies fate specification is well understood, yet quantitative aspects remain to be elucidated. Quantitative models of the netwo...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/9/4/045001
更新日期:2012-08-01 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
pub_type: 杂志文章
doi:10.1088/1478-3975/3/2/006
更新日期:2006-06-23 00:00:00
abstract::Successful biological development via spatial regulation of cell differentiation relies on the action of multiple signaling molecules that are known as morphogens. It is now well-established that signaling molecules create non-uniform concentration profiles, morphogen gradients, that activate different genes, leading ...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/12/2/026006
更新日期:2015-04-17 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
pub_type: 杂志文章,评审
doi:10.1088/1478-3975/3/1/S01
更新日期:2006-02-02 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
pub_type: 杂志文章
doi:10.1088/1478-3975/13/3/036004
更新日期:2016-05-20 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
pub_type: 杂志文章
doi:10.1088/1478-3975/abb209
更新日期:2020-10-21 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
pub_type: 杂志文章
doi:10.1088/1478-3975/8/4/046006
更新日期:2011-08-01 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
pub_type: 杂志文章
doi:10.1088/1478-3975/12/6/066017
更新日期:2015-12-10 00:00:00
abstract::We present a new particle tracking software algorithm designed to accurately track the motion of low-contrast particles against a background with large variations in light levels. The method is based on a polynomial fit of the intensity around each feature point, weighted by a Gaussian function of the distance from th...
journal_title:Physical biology
pub_type: 杂志文章
doi:10.1088/1478-3975/4/3/008
更新日期:2007-10-09 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
pub_type: 杂志文章
doi:10.1088/1478-3975/ab3f5a
更新日期:2019-09-18 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
pub_type: 杂志文章
doi:10.1088/1478-3975/10/4/045005
更新日期:2013-08-01 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
pub_type: 杂志文章
doi:10.1088/1478-3975/5/3/036012
更新日期:2008-09-29 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
pub_type: 杂志文章
doi:10.1088/1478-3967/1/1/004
更新日期:2004-06-01 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
pub_type: 杂志文章
doi:10.1088/1478-3975/9/4/046003
更新日期:2012-08-01 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
pub_type: 杂志文章
doi:10.1088/1478-3975/8/4/046005
更新日期:2011-08-01 00:00:00