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5,600 | Bi-Phasic Vesicles: instability induced by adsorption of proteins | q-bio.SC | The recent discovery of a lateral organization in cell membranes due to small
structures called 'rafts' has motivated a lot of biological and
physico-chemical studies. A new experiment on a model system has shown a
spectacular budding process with the expulsion of one or two rafts when one
introduces proteins on the me... | biology |
5,601 | Turbulence near cyclic fold bifurcations in birhythmic media | q-bio.SC | We show that at the onset of a cyclic fold bifurcation, a birhythmic medium
composed of glycolytic oscillators displays turbulent dynamics. By computing
the largest Lyapunov exponent, the spatial correlation function, and the
average transient lifetime, we classify it as a weak turbulence with transient
nature. Virtual... | biology |
5,602 | Modeling stochastic Ca$^{2+}$ release from a cluster of IP$_3$-sensitive receptors | q-bio.SC | We focused our attention on Ca$^{2+}$ release from the endoplasmic reticulum
through a cluster of inositol 1,4,5-trisphosphate (IP$_3$) receptor channels.
The random opening and closing of these receptors introduce stochastic effects
that have been observed experimentally. Here, we present a stochastic version
of Othme... | biology |
5,603 | Phase Transition in Reconstituted Chromatin | q-bio.SC | By observing reconstituted chromatin by fluorescence microscopy (FM) and
atomic force microscopy (AFM), we found that the density of nucleosomes
exhibits a bimodal profile, i.e., there is a large transition between the dense
and dispersed states in reconstituted chromatin. Based on an analysis of the
spatial distributi... | biology |
5,604 | Pattern formation within Escherichia coli: diffusion, membrane attachment, and self-interaction of MinD molecules | q-bio.SC | In E. coli, accurate cell division depends upon the oscillation of Min
proteins from pole to pole. We provide a model for the polar localization of
MinD based only on diffusion, a delay for nucleotide exchange, and different
rates of attachment to the bare membrane and the occupied membrane. We derive
analytically the ... | biology |
5,605 | Observations of magnetic field induced contraction of fission yeast cells using optical projection microscopy | q-bio.SC | The charges in live cells interact with or produce electric fields, which
results in enormous dielectric responses, flexoelectricity, and related
phenomena. Here we report on a contraction of schizosacchraoymces pombe
(fission yeast) cells induced by magnetic fields, as observed using a phase
sensitive projection image... | biology |
5,606 | Collective charge excitations along cell membranes | q-bio.SC | A significant part of the thin layers of counter-ions adjacent to the
exterior and interior surfaces of a cell membrane form quasi-two-dimensional
(2D) layers of mobile charge. Collective charge density oscillations, known as
plasmon modes, in these 2D charged systems of counter-ions are predicted in the
present paper.... | biology |
5,607 | The dynamics of the min proteins of Escherichia coli under the constant external fields | q-bio.SC | In E. coli the determination of the middle of the cell and the proper
placement of the septum is essential to the division of the cell. This step
depends on the proteins MinC, MinD, and MinE. Exposure to a constant external
field e.g., an electric field or magnetic field may cause the bacteria cell
division mechanism t... | biology |
5,608 | Competing Polymerization of Actin Skeleton explains Relation between Network Polarity and Cell Movements | q-bio.SC | Based on experimental observations it is known that various biological cells
exhibit a persistent random walk during migration on flat substrates. The
persistent random walk is characterized by `stop-and-go' movements :
unidirectional motions over distances of the order of several cell diameter are
separated by localiz... | biology |
5,609 | Uncorrelated two-state single molecule trajectories from reducible kinetic schemes | q-bio.SC | Trajectories of on-off events are the output of many single molecule
experiments. Usually, one describes the underlying mechanism that generates the
trajectory using a kinetic scheme, and by analyzing the trajectory aims at
deducing this scheme. In a previous work [O. Flomenbom, J. Klafter, and A.
Szabo, submitted (200... | biology |
5,610 | Filament depolymerization by motor molecules | q-bio.SC | Motor proteins that specifically interact with the ends of cytoskeletal
filaments can induce filament depolymerization. A phenomenological description
of this process is presented. We show that under certain conditions motors
dynamically accumulate at the filament ends. We compare simulations of two
microscopic models ... | biology |
5,611 | L-selectin mediated leukocyte tethering in shear flow is controlled by multiple contacts and cytoskeletal anchorage facilitating fast rebinding events | q-bio.SC | L-selectin mediated tethers result in leukocyte rolling only above a
threshold in shear. Here we present biophysical modeling based on recently
published data from flow chamber experiments (Dwir et al., J. Cell Biol. 163:
649-659, 2003) which supports the interpretation that L-selectin mediated
tethers below the shear ... | biology |
5,612 | On Myosin II dynamics in the presence of external loads | q-bio.SC | We address the controversial hot question concerning the validity of the
loose coupling versus the lever-arm theories in the actomyosin dynamics by
re-interpreting and extending the phenomenological washboard potential model
proposed by some of us in a previous paper. In this new model a Brownian motion
harnessing ther... | biology |
5,613 | Continuum Description of the Cytoskeleton: Ring Formation in the Cell Cortex | q-bio.SC | Motivated by the formation of ring-like filament structures in the cortex of
plant and animal cells, we study the dynamics of a two-dimensional layer of
cytoskeletal filaments and motor proteins near a surface by a general continuum
theory. As a result of active processes, dynamic patterns of filament
orientation and d... | biology |
5,614 | Modelling and simulation of polycomb-dependent chromosomal interactions in drosophila | q-bio.SC | The conditions of the chromosomes inside the nucleus in the Rabl
configuration have been modelled as self-avoiding polymer chains under
restraining conditions. To ensure that the chromosomes remain stretched out and
lined up, we fixed their end points to two opposing walls. The numbers of
segments $N$, the distances $d... | biology |
5,615 | A Physical Model for the Condensation and Decondensation of Eukaryotic Chromosomes | q-bio.SC | During the eukaryotic cell cycle, chromatin undergoes several conformational
changes, which are believed to play key roles in gene expression regulation
during interphase, and in genome replication and division during mitosis. In
this paper, we propose a scenario for chromatin structural reorganization
during mitosis, ... | biology |
5,616 | Effect of channel block on the spiking activity of excitable membranes in a stochastic Hodgkin-Huxley model | q-bio.SC | The influence of intrinsic channel noise on the spontaneous spiking activity
of poisoned excitable membrane patches is studied by use of a stochastic
generalization of the Hodgkin-Huxley model. Internal noise stemming from the
stochastic dynamics of individual ion channels is known to affect the
collective properties o... | biology |
5,617 | Embryonic Pattern Scaling Achieved by Oppositely Directed Morphogen Gradients | q-bio.SC | Morphogens are proteins, often produced in a localised region, whose
concentrations spatially demarcate regions of differing gene expression in
developing embryos. The boundaries of expression must be set accurately and in
proportion to the size of the one-dimensional developing field; this cannot be
accomplished by a ... | biology |
5,618 | The Water Circuit of the Plants - Do Plants have Hearts ? | q-bio.SC | There is a correspondence between the circulation of blood in all higher
animals and the circulation of sap in all higher plants - up to heights h of
140 m - through the xylem and phloem vessels. Plants suck in water from the
soil, osmotically through the roothair zone, and subsequently lift it
osmotically again, and b... | biology |
5,619 | Kinetic Accessibility of Buried DNA Sites in Nucleosomes | q-bio.SC | Using a theoretical model for spontaneous partial DNA unwrapping from
histones, we study the transient exposure of protein-binding DNA sites within
nucleosomes. We focus on the functional dependence of the rates for site
exposure and reburial on the site position, which is measurable experimentally
and pertinent to gen... | biology |
5,620 | Model for Osteosarcoma-9 as a Potent Factor in Cell Survivor and Resistance to Apoptosis | q-bio.SC | In this paper we use a simple toy model to explore the function of the gene
Osteosarcoma-9. We are in particular interested in understanding the role of
this gene as a potent anti-apoptotic factor. The theoretical description is
constrained by experimental data from induction of apoptosis in cells where
OS-9 is overexp... | biology |
5,621 | Finite-size domains in membranes with active two-state inclusions | q-bio.SC | The distribution of inclusion-rich domains in membranes with active two-state
inclusions is studied by simulations. Our study shows that typical size of
inclusion-rich domains ($L$) can be controlled by inclusion activities in
several ways. When there is effective attraction between state-1 inclusions, we
find: (i) Sma... | biology |
5,622 | Duality, thermodynamics, and the linear programming problem in constraint-based models of metabolism | q-bio.SC | It is shown that the dual to the linear programming problem that arises in
constraint-based models of metabolism can be given a thermodynamic
interpretation in which the shadow prices are chemical potential analogues, and
the objective is to minimise free energy consumption given a free energy drain
corresponding to gr... | biology |
5,623 | The stochastic entry of enveloped viruses: Fusion vs. endocytosis | q-bio.SC | Viral infection requires the binding of receptors on the target cell membrane
to glycoproteins, or ``spikes,'' on the viral membrane. The initial entry is
usually classified as fusogenic or endocytotic. However, binding of viral
spikes to cell surface receptors not only initiates the viral adhesion and the
wrapping pro... | biology |
5,624 | The microtubule transistor | q-bio.SC | I point out the similarity between the microtubule experiment reported by
Priel et al [Biophys. J. 90, 4639 (2006)] and the ZnO nanowire experiment of
Wang et al [Nanolett. 6, 2768 (2006)]. It is quite possible that MTs are
similar to a piezoelectric field effect transistor for which the role of the
control gate electr... | biology |
5,625 | Superdiffusion in a Model for Diffusion in a Molecularly Crowded Environment | q-bio.SC | We present a model for diffusion in a molecularly crowded environment. The
model consists of random barriers in percolation network. Random walks in the
presence of slowly moving barriers show normal diffusion for long times, but
anomalous diffusion at intermediate times. The effective exponents for square
distance ver... | biology |
5,626 | Ion transport through cell membrane channels | q-bio.SC | We discuss various models of ion transport through cell membrane channels.
Recent experimental data shows that sizes of ion channels are compared to those
of ions and that only few ions may be simultaneously in any single channel.
Theoretical description of ion transport in such channels should therefore take
into acco... | biology |
5,627 | Modeling partitioning of Min proteins between daughter cells after septation in Escherichia coli | q-bio.SC | Ongoing sub-cellular oscillation of Min proteins is required to block
minicelling in E. coli. Experimentally, Min oscillations are seen in newly
divided cells and no minicells are produced. In model Min systems many daughter
cells do not oscillate following septation because of unequal partitioning of
Min proteins betw... | biology |
5,628 | Steady-state MreB helices inside bacteria: dynamics without motors | q-bio.SC | Within individual bacteria, we combine force-dependent polymerization
dynamics of individual MreB protofilaments with an elastic model of
protofilament bundles buckled into helical configurations. We use variational
techniques and stochastic simulations to relate the pitch of the MreB helix,
the total abundance of MreB... | biology |
5,629 | Fluctuation analysis of mechanochemical coupling depending on the type of bio-molecular motor | q-bio.SC | Mechanochemical coupling was studied for two different types of myosin motors
in cells: myosin V, which carries cargo over long distances by as a single
molecule; and myosin II, which generates a contracting force in cooperation
with other myosin II molecules. Both mean and variance of myosin V velocity at
various [ATP... | biology |
5,630 | A Symmetry Breaking Model for X Chromosome Inactivation | q-bio.SC | In mammals, dosage compensation of X linked genes in female cells is achieved
by inactivation of one of their two X chromosomes which is randomly chosen. The
earliest steps in X-inactivation (XCI), namely the mechanism whereby cells
count their X chromosomes and choose between two equivalent X, remain
mysterious. Start... | biology |
5,631 | Surfing at the wave fronts: the bidirectional movement of cargo particles driven by molecular motors | q-bio.SC | The collective behavior of molecular motor proteins have been investigated in
the literature using models to describe the long-time dynamics of a
unidimensional continuum motor distribution. Here, we consider the phenomena
related to the transport of particles (vesicles, organelles, virus, etc) in the
realm of these co... | biology |
5,632 | Tug-of-war as a cooperative mechanism for bidirectional cargo transport by molecular motors | q-bio.SC | Intracellular transport is based on molecular motors that pull cargos along
cytoskeletal filaments. One motor species always moves in one direction, e.g.
conventional kinesin moves to the microtubule plus end, while cytoplasmic
dynein moves to the microtubule minus end. However, many cellular cargos are
observed to mov... | biology |
5,633 | Investigating the two-moment characterisation of subcellular biochemical networks | q-bio.SC | While ordinary differential equations (ODEs) form the conceptual framework
for modelling many cellular processes, specific situations demand stochastic
models to capture the influence of noise. The most common formulation of
stochastic models for biochemical networks is the chemical master equation
(CME). While stochas... | biology |
5,634 | A thermodynamic switch for chromosome colocalization | q-bio.SC | A general model for the early recognition and colocalization of homologous
DNA sequences is proposed. We show, on a thermodynamic ground, how the distance
between two homologous DNA sequences is spontaneously regulated by the
concentration and affinity of diffusible mediators binding them, which act as a
switch between... | biology |
5,635 | The dynamics of cargo driven by molecular motors in the context of asymmetric simple exclusion processes | q-bio.SC | We consider the dynamics of cargo driven by a collection of interacting
molecular motors in the context of an asymmetric simple exclusion processes
(ASEP). The model is formulated to account for i) excluded volume interactions,
ii) the observed asymmetry of the stochastic movement of individual motors and
iii) interact... | biology |
5,636 | The switching dynamics of the bacterial flagellar motor | q-bio.SC | Many swimming bacteria are propelled by flagellar motors that stochastically
switch between the clockwise and counterclockwise rotation direction. While the
switching dynamics are one of the most important characteristics of flagellar
motors, the mechanisms that control switching are poorly understood. We present
a sta... | biology |
5,637 | The switching dynamics of the bacterial flagellar motor - Supporting Information | q-bio.SC | In this Supporting information we provide background information on our model
of the bacterial flagellar motor. We also derive the analytical solution of our
coarse-grained model of the switching dynamics and explain the hybrid
stochastic algorithm used for the simulations. | biology |
5,638 | Calculation of the relative metastabilities of proteins in subcellular compartments of Saccharomyces cerevisiae | q-bio.SC | [abridged] Background: The distribution of chemical species in an open system
at metastable equilibrium can be expressed as a function of environmental
variables which can include temperature, oxidation-reduction potential and
others. Calculations of metastable equilibrium for various model systems were
used to charact... | biology |
5,639 | Growth-rate dependent partitioning of RNA polymerases in bacteria | q-bio.SC | Physiological changes which result in changes in bacterial gene expression
are often accompanied by changes in the growth rate for fast adapting enteric
bacteria. Since the availability of RNA polymerase (RNAP) in cells is dependent
on the growth rate, transcriptional control involves not only the regulation of
promote... | biology |
5,640 | Phospholipid demixing and the birth of a lipid droplet | q-bio.SC | The biogenesis of lipid droplets (LD) in the yeast Saccharomyces cerevisiae
was theoretically investigated on basis of a biophysical model. In accordance
with the prevailing model of LD formation, we assumed that neutral lipids
oil-out between the membrane leaflets of the endoplasmic reticulum (ER),
resulting in LD tha... | biology |
5,641 | Nucleocytoplasmic transport: a thermodynamic mechanism | q-bio.SC | The nuclear pore supports molecular communication between cytoplasm and
nucleus in eukaryotic cells. Selective transport of proteins is mediated by
soluble receptors, whose regulation by the small GTPase Ran leads to cargo
accumulation in, or depletion from the nucleus, i.e., nuclear import or nuclear
export. We consid... | biology |
5,642 | Discrete- versus continuous-state descriptions of the F1-ATPase molecular motor | q-bio.SC | A discrete-state model of the F1-ATPase molecular motor is developed which
describes not only the dependences of the rotation and ATP consumption rates on
the chemical concentrations of ATP, ADP, and inorganic phosphate, but also on
mechanical control parameters such as the friction coefficient and the external
torque.... | biology |
5,643 | Predictions from a stochastic polymer model for the MinDE dynamics in E.coli | q-bio.SC | The spatiotemporal oscillations of the Min proteins in the bacterium
Escherichia coli play an important role in cell division. A number of different
models have been proposed to explain the dynamics from the underlying
biochemistry. Here, we extend a previously described discrete polymer model
from a deterministic to a... | biology |
5,644 | Self-organization of the MinE ring in subcellular Min oscillations | q-bio.SC | We model the self-organization of the MinE ring that is observed during
subcellular oscillations of the proteins MinD and MinE within the rod-shaped
bacterium {\it Escherichia coli}. With a steady-state approximation, we can
study the MinE-ring generically -- apart from the other details of the Min
oscillation. Rebindi... | biology |
5,645 | Biophysical mechanism for Ras-nanocluster formation and signaling in plasma membrane | q-bio.SC | Ras GTPases are lipid-anchored G proteins which play a fundamental role in
cell signaling processes. Electron micrographs of immunogold-labeled Ras have
shown that membrane-bound Ras molecules segregate into nanocluster domains.
Several models have been developed in attempts to obtain quantitative
descriptions of nanoc... | biology |
5,646 | In Vivo Localization of Fas-Associated Death Domain Protein in the Nucleus and Cytoplasm of Normal Thyroid and Liver Cells | q-bio.SC | FADD (Fas-associated death domain) is the main death receptor adaptor
molecule that transmits apoptotic signal. Recently, FADD protein was shown to
be expressed both in the cytoplasm and nucleus of in vitro cell lines. In
contrast to the cytoplasmic FADD, the nuclear FADD was shown to protect cells
from apoptosis. Howe... | biology |
5,647 | Self-organized Models of Selectivity in Ca and Na Channels | q-bio.SC | A simple pillbox model with two adjustable parameters accounts for the
selectivity of both DEEA Ca channels and DEKA Na channels in many ionic
solutions of different composition and concentration. Only the side chains are
different in the model of the Ca and Na channels. Parameters are the same for
both channels in all... | biology |
5,648 | Dynamics of intracellular Ca$^{2+}$ oscillations in the presence of multisite Ca$^{2+}$-binding proteins | q-bio.SC | We study the dynamics of intracellular calcium oscillations in the presence
of proteins that bind calcium on multiple sites and that are generally believed
to act as passive calcium buffers in cells. We find that multisite
calcium-binding proteins set a sharp threshold for calcium oscillations. Even
with high concentra... | biology |
5,649 | The Gated Narrow Escape Time for molecular signaling | q-bio.SC | The mean time for a diffusing ligand to activate a target protein located on
the surface of a microdomain can regulate cellular signaling. When the ligand
switches between various states induced by chemical interactions or
conformational changes, while target activation occurs in only one state, this
activation time is... | biology |
5,650 | Modeling torque versus speed, shot noise, and rotational diffusion of the bacterial flagellar motor | q-bio.SC | We present a minimal physical model for the flagellar motor that enables
bacteria to swim. Our model explains the experimentally measured torque-speed
relationship of the proton-driven E. coli motor at various pH and temperature
conditions. In particular, the dramatic drop of torque at high rotation speeds
(the "knee")... | biology |
5,651 | Transient Pulse Formation in Jasmonate Signaling Pathway | q-bio.SC | The jasmonate (JA) signaling pathway in plants is activated as defense
response to a number of stresses like attacks by pests or pathogens and
wounding by animals. Some recent experiments provide significant new knowledge
on the molecular detail and connectivity of the pathway. The pathway has two
major components in t... | biology |
5,652 | Force transduction by the microtubule-bound Dam1 ring | q-bio.SC | The coupling between the depolymerization of microtubules (MTs) and the
motion of the Dam1 ring complex is now thought to play an important role in the
generation of forces during mitosis. Our current understanding of this motion
is based on a number of detailed computational models. Although these models
realize possi... | biology |
5,653 | Phenotypic Heterogeneity in Mycobacterial Stringent Response | q-bio.SC | A common survival strategy of microorganisms subjected to stress involves the
generation of phenotypic heterogeneity in the isogenic microbial population
enabling a subset of the population to survive under stress. In a recent study,
a mycobacterial population of M. smegmatis was shown to develop phenotypic
heterogenei... | biology |
5,654 | Microphase separation in nonequilibrium biomembranes | q-bio.SC | Microphase separation of membrane components is thought to play an important
role in many physiological processes, from cell signaling to endocytosis and
cellular trafficking. Here, we study how variations in the membrane composition
can be driven by fluctuating forces. We show that the membrane steady state is
not onl... | biology |
5,655 | Theoretical analysis of the role of chromatin interactions in long-range action of enhancers and insulators | q-bio.SC | Long-distance regulatory interactions between enhancers and their target
genes are commonplace in higher eukaryotes. Interposed boundaries or insulators
are able to block these long distance regulatory interactions. The mechanistic
basis for insulator activity and how it relates to enhancer
action-at-a-distance remains... | biology |
5,656 | Jamming of molecular motors as a tool for transport cargos along microtubules | q-bio.SC | The hopping model for cargo transport by molecular motors introduced in Refs.
goldman1, goldman2, is extended here in order to incorporate the movement of
cargo-motor complexes. In this context, hopping process expresses the
possibility for cargo to be exchanged between neighbor motors at a microtubule
where the transp... | biology |
5,657 | Toward tunable RNA thermo-switches for temperature dependent gene expression | q-bio.SC | RNA thermometers are mRNA strands with a temperature dependent secondary
structure: depending on the spatial conformation, the mRNA strand can get
translated (on-state) or can be inaccessible for ribosomes binding (off-state).
These have been found in a number of microorganisms (mainly pathogens), where
they are used t... | biology |
5,658 | Branching actin network remodeling governs the force-velocity relationship | q-bio.SC | Actin networks, acting as an engine pushing against an external load, are
fundamentally important to cell motility. A measure of the effectiveness of an
engine is the velocity the engine is able to produce at a given force, the
force-velocity curve. One type of force-velocity curve, consisting of a concave
region where... | biology |
5,659 | Steady-state fluctuations of a genetic feedback loop: an exact solution | q-bio.SC | Genetic feedback loops in cells break detailed balance and involve
bimolecular reactions; hence exact solutions revealing the nature of the
stochastic fluctuations in these loops are lacking. We here consider the master
equation for a gene regulatory feedback loop: a gene produces protein which
then binds to the promot... | biology |
5,660 | Simple variation of the logistic map as a model to invoke questions on cellular protein trafficking | q-bio.SC | Many open problems in biology, as in the physical sciences, display nonlinear
and 'chaotic' dynamics, which, to the extent possible, cannot be reasonably
understood. Moreover, mathematical models which aim to predict/estimate unknown
aspects of a biological system cannot provide more information about the set of
biolog... | biology |
5,661 | Modelling the efficacy of hyperthermia treatment | q-bio.SC | Multimodal oncological strategies which combine chemotherapy or radiotherapy
with hyperthermia have a potential of improving the efficacy of the
non-surgical methods of cancer treatment. Hyperthermia engages the heat-shock
response mechanism (HSR), main component of which are heat-shock proteins
(HSP). Cancer cells hav... | biology |
5,662 | Cooperative dynamics of microtubule ensembles: Polymerization forces and rescue-induced oscillations | q-bio.SC | We investigate the cooperative dynamics of an ensemble of N microtubules
growing against an elastic barrier. Microtubules undergo so-called
catastrophes, which are abrupt stochastic transitions from a growing to a
shrinking state, and rescues, which are transitions back to the growing state.
Microtubules can exert push... | biology |
5,663 | Extremely low-frequency electromagnetic fields cause DNA strand breaks in normal Vero cells | q-bio.SC | Extremely low frequency electromagnetic fields aren't considered as a real
carcinogenic agent despite the fact that some studies have showed impairment of
the DNA integrity in different cells lines. The aim of this study was
evaluation of the late effects of a 100 Hz and 5.6 mT electromagnetic field,
applied continuous... | biology |
5,664 | Comment on "Steady-state fluctuations of a genetic feedback loop: an exact solution" [J. Chem. Phys. {\bf 137}, 035104 (2012).] | q-bio.SC | The comment is intended to answer the criticism presented on `Steady-state
fluctuations of a genetic feedback loop: an exact solution' [J. Chem. Phys.
{\bf 137}, 035104 (2012).] and provides the missing component for the complete
analytic solutions to the author's model. | biology |
5,665 | Dependence of Substrate Irradiation Reaction Rate Stimulation on Lactic Dehydrogenase Source | q-bio.SC | Stimulation of LDH initial reaction rates by timed pre-irradiation of
crystalline sodium pyruvate and lithium lactate is reported for enzymes
isolated from rabbit muscle, pig heart, human erythrocytes and chicken heart.
The phenomenon investigated is referred to as the Comorosan effect. For the
mammalian source enzymes... | biology |
5,666 | Convergence of methods for coupling of microscopic and mesoscopic reaction-diffusion simulations | q-bio.SC | In this paper, three multiscale methods for coupling of mesoscopic
(compartment-based) and microscopic (molecular-based) stochastic
reaction-diffusion simulations are investigated. Two of the three methods that
will be discussed in detail have been previously reported in the literature;
the two-regime method (TRM) and ... | biology |
5,667 | Maxwell's demon for calcium binding to calmodulin? | q-bio.SC | In the recent paper (2011) Faas and co-workers claimed that calmodulin could
directly detect Ca2+ signals by acting as extremely fast calcium buffer.
However the results and their interpretation raise serious doubts about this
conclusion. | biology |
5,668 | Does Plasmodium falciparum have an Achilles' heel? | q-bio.SC | Plasmodium falciparum is the parasite that causes the most severe form of
malaria. Currently, science has been established about its cellular structures,
its metabolic processes, and even the molecular structures of its intrinsic
membrane proteins responsible for transporting water, nutrient, and waste
molecules across... | biology |
5,669 | Bursts of Active Transport in Living Cells | q-bio.SC | We scrutinize the temporally-resolved speed of active cargo transport in
living cells, and show intermittent bursting motions. These nonlinear
fluctuations follow a scaling law over several decades of time and space, the
statistical regularities displaying a time-averaged shape that we interpret to
reflect stress build... | biology |
5,670 | Quantitative analysis of intra-Golgi transport reveals inter-cisternal exchange for all cargo | q-bio.SC | The mechanisms controlling the transport of proteins across the Golgi stack
of mammalian and plant cells is the subject of intense debate, with two models,
cisternal progression and inter-cisternal exchange, emerging as major
contenders. A variety of transport experiments have claimed support for each of
these models. ... | biology |
5,671 | Single molecule enzymology a la Michaelis-Menten | q-bio.SC | In the past one hundred years, deterministic rate equations have been
successfully used to infer enzyme-catalysed reaction mechanisms and to estimate
rate constants from reaction kinetics experiments conducted in vitro. In recent
years, sophisticated experimental techniques have been developed that allow the
measuremen... | biology |
5,672 | Self-regulating genes. Exact steady state solution by using Poisson Representation | q-bio.SC | Systems biology studies the structure and behavior of complex gene regulatory
networks. One of its aims is to develop a quantitative understanding of the
modular components that constitute such networks. The self-regulating gene is a
type of auto regulatory genetic modules which appears in over 40% of known
transcripti... | biology |
5,673 | Biological mechanism and identifiability of a class of stationary conductance model for Voltage-gated Ion channels | q-bio.SC | The physiology of voltage gated ion channels is complex and insights into
their gating mechanism is incomplete. Their function is best represented by
Markov models with relatively large number of distinct states that are
connected by thermodynamically feasible transitions. On the other hand, popular
models such as the ... | biology |
5,674 | Cytoplasmic nanojunctions between lysosomes and sarcoplasmic reticulum are required for specific calcium signaling | q-bio.SC | We demonstrate how nanojunctions between lysosomes and sarcoplasmic reticulum
(L-SR junctions) serve to couple lysosomal activation to regenerative,
ryanodine receptor-mediated cellular calcium (Ca2+) waves. In pulmonary artery
smooth muscle cells (PASMCs) nicotinic acid adenine dinucleotide phosphate
(NAADP) may trigg... | biology |
5,675 | The Long and Viscous Road: Uncovering Nuclear Diffusion Barriers in Closed Mitosis | q-bio.SC | During Saccharomyces cerevisiae closed mitosis, parental identity is
sustained by the asymmetric segregation of ageing factors. Such asymmetry has
been hypothesized to occur via diffusion barriers, constraining protein lateral
exchange in cellular membranes. Diffusion barriers have been extensively
studied in the plasm... | biology |
5,676 | Collective behavior of minus-ended motors in mitotic microtubule asters gliding towards DNA | q-bio.SC | Microtubules (MTs) nucleated by centrosomes form star-shaped structures
referred to as asters. Aster motility and dynamics is vital for genome
stability, cell division, polarization and differentiation. Asters move either
towards the cell center or away from it. Here, we focus on the centering
mechanism in a membrane i... | biology |
5,677 | Effective two-dimensional model does not account for geometry sensing by self-organized proteins patterns - Supplementary document | q-bio.SC | Here we provide a thorough discussion of the model for Min protein dynamics
proposed by Schweizer et al. [11]. The manuscript serves as supplementary
document for our letter to the editor to appear in PNAS. Our analysis is based
on the original COMSOL simulation files that were used for the publication. We
show that al... | biology |
5,678 | Force generation by Myosin II Filaments in Compliant Networks | q-bio.SC | Myosin II isoforms with varying mechanochemistry and filament size interact
with filamentous actin (F-actin) networks to generate contractile forces in
cells. How their properties control force production in environments with
varying stiffness is poorly understood. Here, we incorporated literature values
for properties... | biology |
5,679 | Cell development obeys maximum Fisher information | q-bio.SC | Eukaryotic cell development has been optimized by natural selection to obey
maximal intracellular flux of messenger proteins. This, in turn, implies
maximum Fisher information on angular position about a target nuclear pore
complex (NPR). The cell is simply modeled as spherical, with cell membrane (CM)
diameter 10 micr... | biology |
5,680 | Bistable protein distributions in rod-shaped bacteria | q-bio.SC | The distributions of many proteins in rod-shaped bacteria are far from
homogenous. Often they accumulate at the cell poles or in the cell center. At
the same time, the copy number of proteins in a single cell is relatively small
making the patterns noisy. To explore limits to protein patterns due to
molecular noise, we... | biology |
5,681 | Response to Halatek and Frey: Effective two-dimensional model does account for geometry sensing by self-organized proteins patterns | q-bio.SC | The Min proteins from Escherichia coli can self-organize into traveling waves
on supported lipid bilayers. In Proc. Natl. Acad. Sci. USA 109, 15283 (2012) we
showed that these waves are guided along the boundaries of membrane patches. We
introduced an effective two-dimensional model reproducing the observed
patterns. I... | biology |
5,682 | Influence of Multiplicative Stochastic Variation on Translational Elongation Rates | q-bio.SC | Recent experiments have shown that stochastic effects exerted at the level of
translation contribute a substantial portion of the variation in abundance of
proteins expressed at moderate to high levels. This study analyzes
translational noise arising from fluctuations in residue-specific elongation
rates. The resulting... | biology |
5,683 | Salinity tolerance in plants: attempts to manipulate ion transport | q-bio.SC | Ion transport is the major determining factor of salinity tolerance in
plants. A simple scheme of a plant cell with ion fluxes provides basic
understanding of ion transport and the corresponding changes of ion
concentrations under salinity. The review describes in detail basic principles
of ion transport for a plant ce... | biology |
5,684 | Efficiency of cellular uptake of nanoparticles via receptor-mediated endocytosis | q-bio.SC | Experiments show that cellular uptake of nanoparticles, via receptor-mediated
endocytosis, strongly depends on nanoparticle size. There is an optimal size,
approximately 50 nm in diameter, at which cellular uptake is the highest. In
addition, there is a maximum size, approximately 200 nm, beyond which uptake
via recept... | biology |
5,685 | Accurate chromosome segregation by probabilistic self-organization | q-bio.SC | Background: For faithful chromosome segregation during cell division, correct
attachments must be established between sister chromosomes and microtubules
from opposite spindle poles through kinetochores (chromosome bi-orientation).
Incorrect attachments of kinetochore microtubules (kMTs) lead to chromosome
mis-segregat... | biology |
5,686 | Transcriptional leakage versus noise: A simple mechanism of conversion between binary and graded response in autoregulated genes | q-bio.SC | We study the response of an autoregulated gene to a range of concentrations
of signal molecules. We show that transcriptional leakage and noise due to
translational bursting have the opposite effects. In a positively autoregulated
gene, increasing the noise converts the response from graded to binary, while
increasing ... | biology |
5,687 | New insights on the Dynamic Cellular Metabolism | q-bio.SC | A large number of studies have shown the existence of metabolic covalent
modifications in different molecular structures, able to store biochemical
information that is not encoded by the DNA. Some of these covalent mark
patterns can be transmitted across generations (epigenetic changes). Recently,
the emergence of Hopf... | biology |
5,688 | Stochastic dynamics of virus capsid formation: direct versus hierarchical self-assembly | q-bio.SC | In order to replicate within their cellular host, many viruses have developed
self-assembly strategies for their capsids which are sufficiently robust as to
be reconstituted in vitro. Mathematical models for virus self-assembly usually
assume that the bonds leading to cluster formation have constant reactivity
over the... | biology |
5,689 | Epigenetics: What it is about? | q-bio.SC | Epigenetics has captured the attention of scientists in the past decades, yet
its scope has been continuously changing. In this paper, we give an overview on
how and why its definition has evolved and suggest several clarification on the
concepts used in this field, in particular, on the notions of epigenetic
informati... | biology |
5,690 | Multiscale modeling of exocytosis in the fertilization process | q-bio.SC | We discuss the implementation of a multiscale biophysico-chemical model able
to cope with the main mechanisms underlying cumulative exocytosis in cells. The
model is based on a diffusion equation in the presence of external forces that
links calcium signaling and the biochemistry associated to the activity of
cytoskele... | biology |
5,691 | Mean-field analysis of two-species TASEP with attachment and detachment | q-bio.SC | In cells, most of cargos are transported by motor proteins along microtubule.
Biophysically, unidirectional motion of large number of motor proteins along a
single track can be described by totally asymmetric simple exclusion process
(TASEP). From which many meaningful properties, such as the appearance of
domain wall ... | biology |
5,692 | Bistability: Requirements on Cell-Volume, Protein Diffusion, and Thermodynamics | q-bio.SC | Bistability is considered wide-spread among bacteria and eukaryotic cells,
useful e.g. for enzyme induction, bet hedging, and epigenetic switching.
However, this phenomenon has mostly been described with deterministic dynamic
or well-mixed stochastic models. Here, we map known biological bistable systems
onto the well-... | biology |
5,693 | Contributions to the Theory of Thermostated Systems II: Least Dissipation of Helmholtz Free Energy in Nano-Biology | q-bio.SC | In this paper, we develop further the theory of thermostated systems along
the lines of our earlier paper. Two results are highlighted: 1) in the Markov
limit of the contracted description, a least dissipation of Helmholtz free
energy principle is established; and 2) a detailed account of the
appropriateness of this pr... | biology |
5,694 | Spatial organization of bacterial transcription and translation | q-bio.SC | In bacteria such as $\textit{Escherichia coli}$, DNA is compacted into a
nucleoid near the cell center, while ribosomes$-$molecular complexes that
translate messenger RNAs (mRNAs) into proteins$-$are mainly localized at the
poles. We study the impact of this spatial organization using a minimal
reaction-diffusion model... | biology |
5,695 | Accurate encoding and decoding by single cells: amplitude versus frequency modulation | q-bio.SC | Cells sense external concentrations and, via biochemical signaling, respond
by regulating the expression of target proteins. Both in signaling networks and
gene regulation there are two main mechanisms by which the concentration can be
encoded internally: amplitude modulation (AM), where the absolute concentration
of a... | biology |
5,696 | Asymmetrical inheritance of plasmids depends on dynamic cellular geometry and volume exclusion effects | q-bio.SC | The asymmetrical inheritance of plasmid DNA, as well as other cellular
components, has been shown to be involved in replicative aging. In
Saccharomyces cerevisiae, there is an ongoing debate regarding the mechanisms
underlying this important asymmetry. Currently proposed models suggest it is
established via diffusion, ... | biology |
5,697 | mTORC1 regulates cytokinesis through activation of Rho-ROCK signaling | q-bio.SC | Understanding the mechanisms by which cells coordinate their size with their
ability to divide has long attracted the interest of biologists. The Target of
Rapamycin (TOR) pathway is becoming increasingly recognized as a master
regulator of cell size, however less is known how TOR activity might be coupled
with the cel... | biology |
5,698 | Facilitated diffusion framework for transcription factor search with conformational changes | q-bio.SC | Cellular responses often require the fast activation or repression of
specific genes, which depends on Transcription Factors (TFs) that have to
quickly find the promoters of these genes within a large genome. Transcription
Factors (TFs) search for their DNA promoter target by alternating between bulk
diffusion and slid... | biology |
5,699 | Sequence Heterogeneity Accelerates Protein Search for Targets on DNA | q-bio.SC | The process of protein search for specific binding sites on DNA is
fundamentally important since it marks the beginning of all major biological
processes. We present a theoretical investigation that probes the role of DNA
sequence symmetry, heterogeneity and chemical composition in the protein search
dynamics. Using a ... | biology |
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