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8,900 | Numerical observation of non-axisymmetric vesicles in fluid membranes | physics.bio-ph | By means of Surface Evolver (Exp. Math,1,141 1992), a software package of
brute-force energy minimization over a triangulated surface developed by the
geometry center of University of Minnesota, we have numerically searched the
non-axisymmetric shapes under the Helfrich spontaneous curvature (SC) energy
model. We show ... | physics |
8,901 | Experimental evidence for a power law in electroencephalographic $α$-wave dynamics | physics.bio-ph | We perform an experimental study of the time behavior of the $\alpha$-wave
events occuring in human electroencephalographic signals. We find that the
fraction of the time spent in an $\alpha$-burst of time size $\tau$ exhibits a
scaling behavior as a function of $\tau$. The corresponding exponent is equal
to 1.75$\pm$0... | physics |
8,902 | DNA - Nanoelectronics: Realization of a Single Electron Tunneling Transistor and a Quantum Bit Element | physics.bio-ph | Based on the understanding that chemical bonds can act as tunnel junctions in
the Coulomb blockade regime, and on the technical ability to coat a DNA strand
with metal, we suggest that DNA can be used to built logical devices. We
discuss two explicit examples: a Single Electron Tunneling Transistor (SET) and
a Quantum ... | physics |
8,903 | The Scaling Behaviour of Stochastic Minimization Algorithms in a Perfect Funnel Landscape | physics.bio-ph | We determined scaling laws for the numerical effort to find the optimal
configurations of a simple model potential energy surface (PES) with a perfect
funnel structure that reflects key characteristics of the protein interactions.
Generalized Monte-Carlo methods(MCM, STUN) avoid an enumerative search of the
PES and thu... | physics |
8,904 | A Note on Eye Movement | physics.bio-ph | In a simplified fashion, the motion of the eyeball in its orbit consists of
rotations around a fixed point. Therefore, this motion can be described in
terms of the Euler's angles of rigid body dynamics. However, there is a
physiological constraint in the motion of the eye which reduces to two its
degrees of freedom. Th... | physics |
8,905 | Order parametr for design of proteinlike heteropolymers | physics.bio-ph | preprint withdrawn. A revised version of this paper, with different authors
appears in E. Nelson, P. Wolynes, and J. Onuchic, in Optimization in
computational chemistry and molecular biology, C. Floudas and P. Pardalos
editors, (1999)). The main failing of my approach in these papers is the fact
that the Hamiltonian an... | physics |
8,906 | Structural information from multilamellar liposomes at full hydration: full q-range fitting with high quality X-ray data | physics.bio-ph | We present a novel method for analyzing Small Angle X-ray Scattering data on
multilamellar phospholipid bilayer systems at full hydration. The method
utilizes a modified Caille' theory structure factor in combination with a
Gaussian model representation of the electron density profile such that it
accounts also for the... | physics |
8,907 | X-Ray Kinematography of Temperature-Jump Relaxation Probes the Elastic Properties of Fluid Bilayers | physics.bio-ph | The response kinetics of liquid crystalline phosphatidylcholine bilayer
stacks to rapid, IR-laser induced temperature jumps has been studied by
millisecond time-resolved x-ray diffraction. The system reacts on the fast
temperature change by a discrete bilayer compression normal to its surface and
a lateral bilayer expa... | physics |
8,908 | Physical Aspects of Axonemal Beating and Swimming | physics.bio-ph | We discuss a two-dimensional model for the dynamics of axonemal deformations
driven by internally generated forces of molecular motors. Our model consists
of an elastic filament pair connected by active elements. We derive the dynamic
equations for this system in presence of internal forces. In the limit of small
defor... | physics |
8,909 | The Architecture of Idiotypic Networks: Percolation and Scaling Behaviour | physics.bio-ph | We investigate a model where idiotypes (characterizing B-lymphocytes and
antibodies of an immune system) and anti-idiotypes are represented by
complementary bitstrings of a given length d allowing for a number of
mismatches (matching rules). In this model, the vertices of the hypercube in
dimension d represent the pote... | physics |
8,910 | A Novel Approach to Structure Alignment | physics.bio-ph | A novel approach for structure alignment is presented, where the key
ingredients are: (1) An error function formulation of the problem
simultaneously in terms of binary (Potts) assignment variables and real-valued
atomic coordinates. (2) Minimization of the error function by an iterative
method, where in each iteration... | physics |
8,911 | Information transport by sine-Gordon solitons in microtubules | physics.bio-ph | We study the problem of information propagation in brain microtubules. After
considering the propagation of electromagnetic waves in a fluid of permanent
electric dipoles, the problem reduces to the sine-Gordon wave equation in one
space and one time dimensions. The problem of propagation of information is
thus set. | physics |
8,912 | Large deformation of spherical vesicle studied by perturbation theory and Surface evolver | physics.bio-ph | With tangent angle perturbation approach the axial symmetry deformation of a
spherical vesicle in large under the pressure changes is studied by the
elasticity theory of Helfrich spontaneous curvature model.Three main results in
axial symmetry shape: biconcave shape, peanut shape, and one type of myelin are
obtained. T... | physics |
8,913 | The Cochlear Tuning Curve | physics.bio-ph | The tuning curve of the cochlea measures how large an input is required to
elicit a given output level as a function of the frequency. It is a fundamental
object of auditory theory, for it summarizes how to infer what a sound was on
the basis of the cochlear output. A simple model is presented showing that only
two ele... | physics |
8,914 | Physical Chirality. It Feeds on Negative Entropy | physics.bio-ph | Chirality is considered by many scientists to be mainly a geometric concept.
There exists also a physical aspect of chirality which is largely being
overlooked at. Two examples of mechanical devices are introduced here that
represent ``Physical Chirality''. These are a rotating water sprinkler and a
variant of Crookes'... | physics |
8,915 | Global Spatiotemporal Order and Induced Stochastic Resonance due to a Locally Applied Signal | physics.bio-ph | We study the phenomenon of spatiotemporal stochastic resonance (STSR) in a
chain of diffusively coupled bistable oscillators. In particular, we examine
the situation in which the \textit{global} STSR response is controlled by a
\textit{locally applied signal} and reveal a wave front propagation. In order
to deepen the ... | physics |
8,916 | Longest Life in the Best of Health | physics.bio-ph | Throughout history, for reasons of health, well known personalities have
opted not to eat to satiety - to under-eat - with known benefits. Here, for the
benefits of under-eating a very simple explanation is offered and discussed in
some detail. Our distant ancestors, whose bodies we inherited, ate and weighed
a good de... | physics |
8,917 | A continuous isotropic-nematic liquid crystalline transition of F-actin solutions | physics.bio-ph | The phase transition from the isotropic (I) to nematic (N) liquid crystalline
suspension of F-actin of average length $3~\mu$m or above was studied by local
measurements of optical birefringence and protein concentration. Both
parameters were detected to be continuous in the transition region, suggesting
that the I-N t... | physics |
8,918 | Temperature dependence of optical rotation study on parity-violating phase transition of D-, L-, and DL-alanine | physics.bio-ph | Chiral molecules are characterized by a specific optical rotation angle. An
experimental method was presented to dissect the temperature dependence of the
optical rotation angle with the molecular chirality of D-alanine, L-alanine and
DL-alanine crystals. Salam hypothesis predicted that quantum mechanical
cooperative a... | physics |
8,919 | On the writhe of non-closed curves | physics.bio-ph | The writhe of a space curve fragment is considered for various boundary
conditions. An expression for the writhe as a function of arclength for an
arbitrary space curve is obtained. The formula is built on the base of closing
the tangent indicatrix with a geodesic. The corresponding closure of a curve in
3-space is exp... | physics |
8,920 | Treatment of skin deseases in humans by a new method | physics.bio-ph | The original method of treatment of various pathological processes in human
skin covers is described. The method has a brightly expressed differential
action: destroying pathologic cells it does not render any influence on healthy
cells. The examples of application of a method for treatment of some kinds of
skin pathol... | physics |
8,921 | Network Landscape from a Brownian Particle's Perspective | physics.bio-ph | Given a complex biological or social network, how many clusters should it be
decomposed into? We define the distance $d_{i,j}$ from node $i$ to node $j$ as
the average number of steps a Brownian particle takes to reach $j$ from $i$.
Node $j$ is a global attractor of $i$ if $d_{i,j}\leq d_{i,k}$ for any $k$ of
the graph... | physics |
8,922 | Motion of an Adhesive Gel in a Swelling Gradient: a Mechanism for Cell Locomotion | physics.bio-ph | Motivated by the motion of nematode sperm cells, we present a model for the
motion of an adhesive gel on a solid substrate. The gel polymerizes at the
leading edge and depolymerizes at the rear. The motion results from a
competition between a self-generated swelling gradient and the adhesion on the
substrate. The resul... | physics |
8,923 | An Estimate of the Vibrational Frequencies of Spherical Virus Particles | physics.bio-ph | The possible normal modes of vibration of a nearly spherical virus particle
are discussed. Two simple models for the particle are treated, a liquid drop
model and an elastic sphere model. Some estimates for the lowest vibrational
frequency are given for each model. It is concluded that this frequency is
likely to be of... | physics |
8,924 | Two-vibron bound states in alpha-helix proteins : the interplay between the intramolecular anharmonicity and the strong vibron-phonon coupling | physics.bio-ph | The influence of the intramolecular anharmonicity and the strong
vibron-phonon coupling on the two-vibron dynamics in an $\alpha$-helix protein
is studied within a modified Davydov model. The intramolecular anharmonicity of
each amide-I vibration is considered and the vibron dynamics is described
according to the small... | physics |
8,925 | Current Reversals in a inhomogeneous system with asymmetric unbiased fluctuations | physics.bio-ph | We present a study of transport of a Brownian particle moving in periodic
symmetric potential in the presence of asymmetric unbiased fluctuations. The
particle is considered to move in a medium with periodic space dependent
friction. By tuning the parameters of the system, the direction of current
exhibit reversals, bo... | physics |
8,926 | Relaxation channels of two-vibron bound states in α-helix proteins | physics.bio-ph | Relaxation channels for two-vibron bound states in an anharmonic alpha-helix
protein are studied. It is pointed out that the relaxation originates in the
interaction between the dressed anharmonic vibrons and the remaining phonons.
This interaction is responsible for the occurrence of transitions between
two-vibron eig... | physics |
8,927 | Panic induced symmetry breaking in escaping ants | physics.bio-ph | We report the phenomenon of symmetry breaking in ants escaping under panic.
Ants confined into a cell with two symmetrically located exits use both exits
in approximately equal proportions to abandon the cell in normal conditions,
but prefer one of the exits if panic is created by adding a repellent fluid.
This finding... | physics |
8,928 | An analytical analysis of vesicle tumbling under a shear flow | physics.bio-ph | Vesicles under a shear flow exhibit a tank-treading motion of their membrane,
while their long axis points with an angle < 45 degrees with respect to the
shear stress if the viscosity contrast between the interior and the exterior is
not large enough. Above a certain viscosity contrast, the vesicle undergoes a
tumbling... | physics |
8,929 | Molecular Dynamics Simulation of Amyloid Beta Dimer Formation | physics.bio-ph | Recent experiments with amyloid-beta (Abeta) peptide suggest that formation
of toxic oligomers may be an important contribution to the onset of Alzheimer's
disease. The toxicity of Abeta oligomers depends on their structure, which is
governed by assembly dynamics. Due to limitations of current experimental
techniques, ... | physics |
8,930 | Measuring the force ejecting DNA from phage | physics.bio-ph | We discuss how a balance can be established between the force acting to eject
DNA from viral capsids and the force resisting its entry into a colloidal
suspension which mimics the host cell cytoplasm. The ejection force arises from
the energy stored in the capsid as a consequence of the viral genome
(double-stranded DN... | physics |
8,931 | Comment on Why is the DNA Transition First Order? and Griffiths Singularities in Unbinding of Strongly Disordered Polymers | physics.bio-ph | The papers [1,2] consider unbinding of a disordered heteropolymer. They find
the first order phase transition [1] when disorder is strong (i.e. the ratio v
of the binding energies is large; in DNA v is~1.1) and the Griffiths
singularity, i.e. infinite order transition, otherwise [2]. The problem is
important, since man... | physics |
8,932 | Dynamics of Human Walking | physics.bio-ph | The problem of biped locomotion at steady speeds is discussed through a
Lagrangian formulation developed for velocity-dependent, body driving forces.
Human walking on a level surface is analyzed in terms of the data on the
resultant ground-reaction force and the external work. It is shown that the
trajectory of the cen... | physics |
8,933 | Modifications of the Dielectric Properties of Biological Membranes by Heating | physics.bio-ph | Biological cell suspensions are known to show dielectric dispersions due to
the Maxwell-Wagner mechanism. Many examples are summarized in a number of
papers by Schwan [7, 9, 10]. By the application of an appropriate analysis to
the dielectric dispersion, it is possible to estimate electrical phase
parameters related to... | physics |
8,934 | Coupled dynamics of voltage and calcium in paced cardiac cells | physics.bio-ph | We investigate numerically and analytically the coupled dynamics of
transmembrane voltage and intracellular calcium cycling in paced cardiac cells
using a detailed physiological model and its reduction to a three-dimensional
discrete map. The results provide a theoretical framework to interpret various
experimentally o... | physics |
8,935 | Structural Effects of Small Molecules on Phospholipid Bilayers Investigated by Molecular Simulations | physics.bio-ph | We summarize and compare recent Molecular Dynamics simulations on the
interactions of dipalmitoylphosphatidylcholine (DPPC) bilayers in the liquid
crystalline phase with a number of small molecules including trehalose, a
disaccharide of glucose, alcohols, and dimethylsulfoxide (DMSO). The sugar
molecules tend to stabil... | physics |
8,936 | Where To Go and How To Go: a Theoretical Study of Different Leader Roles in Networked Systems | physics.bio-ph | This letter studies synchronization conditions for distributed dynamic
networks with different types of leaders. The role of a leader specifying a
desired global state trajectory through local interactions (the power leader)
has long been recognized and modeled. This paper introduces the complementary
notion of a knowl... | physics |
8,937 | Quantitative photoluminescence of broad band absorbing melanins: A procedure to correct for inner filter and re-absorption effects | physics.bio-ph | We report methods for correcting the photoluminescence emission and
excitation spectra of highly absorbing samples for re-absorption and inner
filter effects. We derive the general form of the correction, and investigate
various methods for determining the parameters. Additionally, the correction
methods are tested wit... | physics |
8,938 | Engines at molecular scales | physics.bio-ph | In recent literature there has been a lot of interest in the phenomena of
noise induced transport in the absence of an average bias occurring in
spatially periodic systems far from equilibrium. One of the main motivations in
this area is to understand the mechanism behind the operation of biological
motors at molecular... | physics |
8,939 | Statistical mechanics of columnar DNA assemblies | physics.bio-ph | Many physical systems can be mapped onto solved or "solvable" models of
magnetism. In this work, we have mapped the statistical mechanics of columnar
phases of ideally helical rigid DNA -- subject to the earlier found unusual,
frustrated pair potential [A. A. Kornyshev and S. Leikin, J. Chem. Phys. 107,
3656 (1997)] --... | physics |
8,940 | Phase Separation of Saturated and Mono-unsaturated Lipids as determined from a Microscopic Model | physics.bio-ph | A molecular model is proposed of a bilayer consisting of fully saturated DPPC
and mono unsaturated DOPC. The model not only encompasses the constant density
within the hydrophobic core of the bilayer, but also the tendency of chain
segments to align. It is solved within self-consistent field theory. A model
bilayer of ... | physics |
8,941 | Counterion density profiles at charged flexible membranes | physics.bio-ph | Counterion distributions at charged soft membranes are studied using
perturbative analytical and simulation methods in both weak coupling
(mean-field or Poisson-Boltzmann) and strong coupling limits. The softer the
membrane, the more smeared out the counterion density profile becomes and
counterions pentrate through th... | physics |
8,942 | Multifractal Analysis of Human Retinal Vessels | physics.bio-ph | In this work it is shown that vascular structures of the human retina
represent geometrical multifractals, characterized by a hierarchy of exponents
rather then a single fractal dimension. A number of retinal images from the
STARE database (www.parl.clemson.edu/stare) are analyzed, corresponding to both
normal and path... | physics |
8,943 | Spatial snowdrift game with myopic agents | physics.bio-ph | We have studied a spatially extended snowdrift game, in which the players are
located on the sites of two-dimensional square lattices and repeatedly have to
choose one of the two strategies, either cooperation (C) or defection (D). A
player interacts with its nearest neighbors only, and aims at playing a
strategy which... | physics |
8,944 | Atomic transfers between implanted bioceramics and tissues in orthopaedics surgery | physics.bio-ph | We study transfers of ions and debris from bioceramics implanted in bone
sites. A contamination of surrounding tissues may play a major role in aseptic
loosening of the implant. For these reasons, bioceramics require studies of
biocompatibility and biofunctionality . So, in addition to in vitro studies of
bioceramics, ... | physics |
8,945 | Random walk and balancing | physics.bio-ph | Presents a minireview of topics concerned with balancing in quiet (bipedal)
standing, and balancing of a stick. In the focus is the apparent stochastic
nature of the swaying of the human inverted pendulum. | physics |
8,946 | Probing Dynamics at Interfaces: Molecular Motions in Lipid Bilayers studied by Neutron Backscattering | physics.bio-ph | Lipid membranes in a physiological context cannot be understood without
taking into account their mobile environment. Here, we report on a high
energy-resolution neutron backscattering study to investigate slow motions on
nanosecond time scales in highly oriented solid supported phospholipid bilayers
of the model syste... | physics |
8,947 | Probing Dynamics at Interfaces: Options for Neutron and X-ray Spectroscopy | physics.bio-ph | Inelastic neutron and X-ray scattering experiments on surfaces and interfaces
are a challenging topic in modern physics. Particular interest arises regarding
surfaces and interfaces of soft matter and biological systems. We review both
neutron and x-ray spectroscopic techniques with view at their applicability to
these... | physics |
8,948 | Stochastic Dynamics of Magnetosomes in Cytoskeleton | physics.bio-ph | Rotations of microscopic magnetic particles, magnetosomes, embedded into the
cytoskeleton and subjected to the influence of an ac magnetic field and thermal
noise are considered. Magnetosome dynamics is shown to comply with the
conditions of the stochastic resonance under not-too-tight constraints on the
character of t... | physics |
8,949 | Peptide Conformational Equilibria Computed via a Single-Stage Shifting Protocol | physics.bio-ph | We study the conformational equilibria of two peptides using a novel
statistical mechanics approach designed for calculating free energy differences
between highly dis-similar conformational states. Our results elucidate the
contrasting roles of entropy in implicitly solvated leucine dipeptide and
decaglycine. The meth... | physics |
8,950 | X-ray microanalysis in STEM of short-term physico-chemical reactions at bioactive glass particles / biological fluids interface. Determination of O/Si atomic ratios | physics.bio-ph | Short-term physico-chemical reactions at the interface between bioactive
glass particles and biological fluids are studied and we focus our attention on
the measurements of O/Si atomic ratio. The studied bioactive glass is in the
SiO2-Na2O-CaO-P2O5-K2O-Al2O3-MgO system. The elemental analysis is performed at
the submic... | physics |
8,951 | Stochastic dynamics of magnetic nanoparticles and a mechanism of biological orientation in the geomagnetic field | physics.bio-ph | The rotations of microscopic magnetic particles, magnetosomes, embedded into
the cytoskeleton are considered. A great number of magnetosomes are shown to
possess two stable equilibrium positions, between which there occur transitions
under the influence of thermal disturbances. The random rotations attain the
value of ... | physics |
8,952 | Photosystem 0, a proposed ancestral photosystem without reducing power that synthesized ATP during light-dark cycling | physics.bio-ph | Photosystem 0 concerns a primitive mechanism for free energy gain as ATP from
fluctuating light during early evolution. The PS0 reaction centers had no
reducing power: charge transport was only temporary. Light induced within the
reaction centers metastable dipoles that generated a membrane potential. This
in turn drov... | physics |
8,953 | Vibron-polaron in alpha-helices. I. Single-vibron states | physics.bio-ph | The vibron dynamics associated to amide-I vibrations in a 3D alpha-helix is
described according to a generalized Davydov model. The helix is modeled by
three spines of hydrogen-bonded peptide units linked via covalent bonds. To
remove the intramolecular anharmonicity of each amide-I mode and to
renormalized the vibron-... | physics |
8,954 | Contamination by metallic elements released from joint prostheses | physics.bio-ph | When a metallic implant is in contact with human tissues, the organism reacts
and a corrosion process starts. Consequently, we might observe liberation of
metallic debris and wear. Our purpose is to measure the contamination and the
migration of these metallic elements in the surrounding tissues of the implant.
Two typ... | physics |
8,955 | Gel Electrophoresis of DNA Knots in Weak and Strong Electric Fields | physics.bio-ph | Gel electrophoresis allows to separate knotted DNA (nicked circular) of equal
length according to the knot type. At low electric fields, complex knots being
more compact, drift faster than simpler knots. Recent experiments have shown
that the drift velocity dependence on the knot type is inverted when changing
from low... | physics |
8,956 | Tumor growth instability and the onset of invasion | physics.bio-ph | Motivated by experimental observations, we develop a mathematical model of
chemotactically directed tumor growth. We present an analytical study of the
model as well as a numerical one. The mathematical analysis shows that: (i)
tumor cell proliferation by itself cannot generate the invasive branching
behaviour observed... | physics |
8,957 | Morphological Variation in a Toroid Generated from a Single Polymer Chain | physics.bio-ph | A single semiflexible polymer chain folds into a toroidal object under poor
solvent conditions. In this study, we examined the morphological change in such
a toroidal state as a function of the width and stiffness of the chain together
with the surface energy, which characterizes the segmental interaction
parameter. Ch... | physics |
8,958 | A model for codon position bias in RNA editing | physics.bio-ph | RNA editing can be crucial for the expression of genetic information via
inserting, deleting, or substituting a few nucleotides at specific positions in
an RNA sequence. Within coding regions in an RNA sequence, editing usually
occurs with a certain bias in choosing the positions of the editing sites. In
the mitochondr... | physics |
8,959 | Scale dependence of branching in arterial and bronchial trees | physics.bio-ph | Although models of branching in arterial and bronchial trees often predict a
dependence of bifurcation parameters on the scale of the bifurcating vessels,
direct verifications of this dependence with data are uncommon. We compare
measurements of bifurcation parameters in airways and arterial trees of
different mammals ... | physics |
8,960 | Towards Experimental Tests of Quantum Effects in Cytoskeletal Proteins | physics.bio-ph | It has become increasingly evident that fabrication of novel biomaterials
through molecular self-assembly is going to play a significant role in material
science and possibly the information technology of the future. Tubulin,
microtubules (MTs) and the cytoskeleton are dynamic, self-assembling systems
and we asked whet... | physics |
8,961 | Theory and Experiments on the "Quantum Mind" | physics.bio-ph | This article is a short summary, in Greek, of work presented in English in
the following articles:
1. Mershin et al. "Towards Experimental Tests of Quantum Effects in
Cytoskeletal Proteins" (physics/0505080)
2. Mershin et al. "Learning and Memory deficits Upon TAU Accumulation in
Drosophila Mushroom Body Neurons", ... | physics |
8,962 | The use of a syncytium model of the crystalline lens of the human eye to study the light flashes seen by astronauts | physics.bio-ph | A syncytium model to study some electrical properties of the eye is proposed
in the attempt to explain the phenomenon of anomalous Light Flashes (LF)
perceived by astronauts in orbit. The crystalline lens is modelled as an
ellipsoidal syncytium having a variable relative dielectric constant. The
mathematical model prop... | physics |
8,963 | Elasticity Theory and Shape Transitions of Viral Shells | physics.bio-ph | Recently, continuum elasticity theory has been applied to explain the shape
transition of icosahedral viral capsids - single-protein-thick crystalline
shells - from spherical to buckled/faceted as their radius increases through a
critical value determined by the competition between stretching and bending
energies of a ... | physics |
8,964 | A modelling approach towards Epidermal homoeostasis control | physics.bio-ph | In order to grasp the features arising from cellular discreteness and
individuality, in large parts of cell tissue modelling agent-based models are
favoured. The subclass of off-lattice models allows for a physical motivation
of the intercellular interaction rules. We apply an improved version of a
previously introduce... | physics |
8,965 | Extracellular polymeric bacterial coverages as minimal area surfaces | physics.bio-ph | Surfaces formed by extracellular polymeric substances enclosing individual
and some small communities of {\it Acidithiobacillus ferrooxidans} on plates of
hydrophobic silicon and hydrophilic mica are analyzed by means of atomic force
microscopy imaging. Accurate nanoscale descriptions of such coverage surfaces
are obta... | physics |
8,966 | Stochastic resonance in the growth of a tumor induced by correlated noises | physics.bio-ph | Multiplicative noise is found to divide the growth law of tumors into two
parts in a logistic model, which is driven by additive and multiplicative
noises simultaneously. The Fokker-Planck equation was also derived to explain
the fact that the influence of the intensity of multiplicative noise on the
growth of tumor ce... | physics |
8,967 | Lancret helices | physics.bio-ph | Helical configurations of inhomogeneous symmetric rods with non-constant
bending and twisting stiffness are studied within the framework of the
Kirchhoff rod model. From the static Kirchhoff equations, we obtain a set of
differential equations for the curvature and torsion of the centerline of the
rod and the Lancret's... | physics |
8,968 | What can we learn about the lipid vesicle structure from the small-angle neutron scattering experiment? (Investigation DMPC vesicle structure by small angle neutron scattering) | physics.bio-ph | Small angle neutron scattering (SANS) on the unilamellar vesicle populations
(diameter 500 and 1000 angstrom) was used to characterize lipid vesicles from
dimyristoylphosphatidylcholine (DMPC) at three phases (gel, ripple, and
liquid). Parameters of vesicle populations and internal structure of the DMPC
bilayer were ch... | physics |
8,969 | Phase diagram of a ternary mixture of cholesterol and saturated and unsaturated lipids calculated from a microscopic model | physics.bio-ph | We employ a molecular model to study a ternary mixture of saturated lipid,
with tails of sixteen carbons, a mono unsaturated lipid with tails of eighteen
carbons, and cholesterol. The model, solved within mean-field theory, produces
several forms of phase diagrams depending upon the relative strengths of
interactions, ... | physics |
8,970 | Dynamical model based on finite stacking enthalpies for homogeneous and inhomogeneous DNA thermal denaturation | physics.bio-ph | We present a nonlinear dynamical model for DNA thermal denaturation, which is
based on the finite stacking enthalpies used in thermodynamical
nearest-neighbour calculations. Within this model, the finiteness of stacking
enthalpies is shown to be responsible for the sharpness of calculated melting
curves. Transfer-integ... | physics |
8,971 | Comparison of metal-amino acid interaction in Phe-Ag and Tyr-Ag complexes by spectroscopic measurements | physics.bio-ph | In this article, we have compared the metal-amino acid interactions in Tyr-Ag
and Phe-Ag complexes through pH dependent SERS measurements. By analyzing the
variation in relative intensities of SERS bands with the pH of the amino acid
solution, we have obtained the orientation and conformation of the amino acid
molecule... | physics |
8,972 | Role of network connectivity in intercellular calcium oscillations | physics.bio-ph | It is important to understand the coordinated performance of cells in tissue.
One possible mechanism in this coordination involves intracellular calcium
signaling. The topology of intercellular connections in tissue should also play
an important role in this process. It is most relevant for plane tissues, in
which the ... | physics |
8,973 | An elasticity theory for self-assembled protein lattices with application to the martensitic phase transition in bacteriophage T4 tail sheath | physics.bio-ph | We propose an elasticity theory for one and two dimensional arrays of
globular proteins for which the free energy is affected by relative position
and relative rotation between neighboring molecules. The kinematics of such
assemblies is described, the conditions of compatibility are found, a form of
the free energy is ... | physics |
8,974 | Vibron-polaron in alpha-helices. II. Two-vibron bound states | physics.bio-ph | The two-vibron dynamics associated to amide-I vibrations in a 3D
$\alpha$-helix is described according to a generalized Davydov model. The helix
is modeled by three spines of hydrogen-bonded peptide units linked via covalent
bonds. It is shown that the two-vibron energy spectrum supports both a
two-vibron free states c... | physics |
8,975 | Characteristic Length Scale of Electric Transport Properties of Genomes | physics.bio-ph | A tight-binding model together with a novel statistical method are used to
investigate the relation between the sequence-dependent electric transport
properties and the sequences of protein-coding regions of complete genomes. A
correlation parameter $\Omega$ is defined to analyze the relation. For some
particular propa... | physics |
8,976 | Monte Carlo simulation of melting transition on DNA nanocompartment | physics.bio-ph | DNA nanocompartment is a typical DNA-based machine whose function is
dependent of molecular collective effect. Fundamental properties of the device
have been addressed via electrochemical analysis, fluorescent microscopy, and
atomic force microscopy. Interesting and novel phenomena emerged during the
switching of the d... | physics |
8,977 | Chaotic desynchronization of multi-strain diseases | physics.bio-ph | Multi-strain diseases are diseases that consist of several strains, or
serotypes. The serotypes may interact by antibody-dependent enhancement (ADE),
in which infection with a single serotype is asymptomatic, but infection with a
second serotype leads to serious illness accompanied by greater infectivity. It
has been o... | physics |
8,978 | Johnson-Kendall-Roberts theory applied to living cells | physics.bio-ph | Johnson-Kendall-Roberts (JKR) theory is an accurate model for strong adhesion
energies of soft slightly deformable material. Little is known about the
validity of this theory on complex systems such as living cells. We have
addressed this problem using a depletion controlled cell adhesion and measured
the force necessa... | physics |
8,979 | Coarse-graining protein energetics in sequence variables | physics.bio-ph | We show that cluster expansions (CE), previously used to model solid-state
materials with binary or ternary configurational disorder, can be extended to
the protein design problem. We present a generalized CE framework, in which
properties such as energy can be unambiguously expanded in the amino-acid
sequence space. T... | physics |
8,980 | Migration induced epidemics: Dynamics of flux-based multipatch models | physics.bio-ph | Classical disease models use a mass action term as the interaction between
infected and susceptible people in separate patches. We derive the equations
when this interaction is a migration of people between patches. The results
model what happens when a new population is moved into a region with endemic
disease. | physics |
8,981 | DNA properties investigated by dynamic force microscopy | physics.bio-ph | In this work, we show that by varying the experimental conditions, the
driving amplitude, a dynamic force microscope allows DNA properties to be
selectively imaged. The substrate on which the DNA is fixed is a silica surface
grafted with silanes molecules ended with amine groups. Use of small
oscillation amplitudes fav... | physics |
8,982 | The stability of solitons in biomembranes and nerves | physics.bio-ph | We examine the stability of a class of solitons, obtained from a
generalization of the Boussinesq equation, which have been proposed to be
relevant for pulse propagation in biomembranes and nerves. These solitons are
found to be stable with respect to small amplitude fluctuations. They emerge
naturally from non-soliton... | physics |
8,983 | A phenomenological approach to the simulation of metabolism and proliferation dynamics of large tumour cell populations | physics.bio-ph | A major goal of modern computational biology is to simulate the collective
behaviour of large cell populations starting from the intricate web of
molecular interactions occurring at the microscopic level. In this paper we
describe a simplified model of cell metabolism, growth and proliferation,
suitable for inclusion i... | physics |
8,984 | Facilitated diffusion of DNA-binding proteins: Efficient simulation with the method of excess collisions (MEC) | physics.bio-ph | In this paper, a new method to efficiently simulate diffusion controlled
second order chemical reactions is derived and applied to site-specific
DNA-binding proteins. The protein enters a spherical cell and propagates via
two competing modes, a free diffusion and a DNA-sliding mode, to search for its
specific binding s... | physics |
8,985 | Model of Low-pass Filtering of Local Field Potentials in Brain Tissue | physics.bio-ph | Local field potentials (LFPs) are routinely measured experimentally in brain
tissue, and exhibit strong low-pass frequency filtering properties, with high
frequencies (such as action potentials) being visible only at very short
distances ($\approx$10~$\mu m$) from the recording electrode. Understanding
this filtering i... | physics |
8,986 | Hydrosomes: Optically trapped femtoliter containers for single molecule studies and microfluidics | physics.bio-ph | We demonstrate a novel technique for creating, manipulating, and combining
femtoliter volume chemical containers. Possible uses include creating
controlled chemical reactions involving small quantities of reagent, and
studying the dynamics of single molecules within the containers by fluorescence
imaging techniques. Th... | physics |
8,987 | Torsional fluctuations in columnar DNA assemblies | physics.bio-ph | In columnar assemblies of helical bio-molecules the azimuthal degrees of
freedom, i.e. rotations about the long axes of molecules, may be important in
determining the structure of the assemblies especially when the interaction
energy between neighbouring molecules explicitly depends on their relative
azimuthal orientat... | physics |
8,988 | Conditions for propagation and block of excitation in an asymptotic model of atrial tissue | physics.bio-ph | Detailed ionic models of cardiac cells are difficult for numerical
simulations because they consist of a large number of equations and contain
small parameters. The presence of small parameters, however, may be used for
asymptotic reduction of the models. Earlier results have shown that the
asymptotics of cardiac equat... | physics |
8,989 | Role of fluctuations in a snug-fit mechanism of KcsA channel selectivity | physics.bio-ph | The KcsA potassium channel belongs to a class of K+ channels that is
selective for K+ over Na+ at rates of K+ transport approaching the diffusion
limit. This selectivity is explained thermodynamically in terms of favorable
partitioning of K+ relative to Na+ in a narrow selectivity filter in the
channel. One mechanism f... | physics |
8,990 | Detailed analysis of the response of different cell lines to carbon irradiation | physics.bio-ph | Published survival data for Chinese hamster ovarian cells CHO-K1 and their
radiosensitive mutant xrs5 after irradiation by carbon ions of energies from
2.4 to 266.4 MeV/u have been analyzed using the probabilistic two-stage
radiobiological model, which enables to represent the interplay of damage
induction and repair p... | physics |
8,991 | Motion of the hydrogen bond proton in cytosine and the transition between its normal and imino states | physics.bio-ph | The potential energy surface of the H13 proton in base cytosine of the DNA
molecules is calculated {\it ab initio} at the Gaussian98 MP2/6-311G(d,p)
level. Two potential wells are found. One corresponds to the normal cytosine,
while the other corresponds to its imino tautomer. The bindings of the proton
in these wells ... | physics |
8,992 | Towards more realistic dynamical models for DNA secondary structure | physics.bio-ph | We propose a dynamical model for the secondary structure of DNA, which is
based on the finite stacking enthalpies used in thermodynamics calculations. In
this model, the two strands can separate and the bases are allowed to rotate
perpendicular to the sequence axis. We show, through molecular dynamics
simulations, that... | physics |
8,993 | Inferring mixed-culture growth from total biomass data in a wavelet approach | physics.bio-ph | It is shown that the presence of mixed-culture growth in batch fermentation
processes can be very accurately inferred from total biomass data by means of
the wavelet analysis for singularity detection. This is accomplished by
considering simple phenomenological models for the mixed growth and the more
complicated case ... | physics |
8,994 | Swimming Efficiency of Bacterium Escherichia Coli | physics.bio-ph | We use in vivo measurements of swimming bacteria in an optical trap to
determine fundamental properties of bacterial propulsion. In particular, we
determine the propulsion matrix, which relates the angular velocity of the
flagellum to the torques and forces propelling the bacterium. From the
propulsion matrix dynamical... | physics |
8,995 | A Classification Scheme for Phenomenological Universalities in Growth Problems | physics.bio-ph | A classification in universality classes of broad categories of
phenomenologies, belonging to different disciplines, may be very useful for a
crossfertilization among them and for the purpose of pattern recognition. We
present here a simple scheme for the classification of nonlinear growth
problems. The success of the ... | physics |
8,996 | Channel noise and synchronization in excitable membranes | physics.bio-ph | Using a stochastic generalization of the Hodgkin–Huxley model, we
consider the influence of intrinsic channel noise on the synchronization
between the spiking activity of the excitable membrane and an externally
applied periodic signal. For small patches, i.e., when the channel noise
dominates the excitable dynam... | physics |
8,997 | Non-Markovian Stochastic Resonance: three state model of ion channel gating | physics.bio-ph | Stochastic Resonance in single voltage-dependent ion channels is investigated
within a three state non-Markovian modeling of the ion channel conformational
dynamics. In contrast to a two-state description one assumes the presence of an
additional closed state for the ion channel which mimics the manifold of
voltage-ind... | physics |
8,998 | The role of conformational diffusion in ion channel gating | physics.bio-ph | We consider an exactly tractable model of the Kramers type for the
voltage-dependent gating dynamics of single ion channels. It is assumed that
the gating dynamics is caused by the thermally activated transitions in a
bistable potential. Moreover, the closed state of the channel is highly
degenerate and embraces the wh... | physics |
8,999 | Cytoskeleton influence on normal and tangent fluctuation modes in the red blood cells | physics.bio-ph | We argue that the paradoxal softness of the red blood cells (RBC) in
fluctuation spectra experiments is apparent. We show that the effective surface
shear modulus $\mu_s$ of the RBC obtained from fluctuation data and that
measured in static deformation experiments have the same order of magnitude. A
simple micromechani... | physics |
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