Information: currency of life?
Daniel Polani
In biology, the exception is mostly the rule, and the rule is mostly the exception. However, recent results indicate that known universal concepts in biology such as the genetic code or the utilization of ATP as a source of energy may be complemented by a large class of principles based on Shannon's ... [HFSP J. 3, 307 (2009)] published Thu Nov 12, 2009.
Chaoticity of the blood cell production system
Ryszard Rudnicki
We present a structured model of stem cells given by a partial differential equation. This equation generates a semiflow acting on the set of densities. We show that this semiflow possesses an invariant exact measure positive on open sets. From this it follows that the system is chaotic, i.e., it ha ... [Chaos 19, 043112 (2009)] published Fri Nov 6, 2009.
Accurate noise projection for reduced stochastic epidemic models
Eric Forgoston, Lora Billings, and Ira B. Schwartz
We consider a stochastic susceptible-exposed-infected-recovered (SEIR) epidemiological model. Through the use of a normal form coordinate transform, we are able to analytically derive the stochastic center manifold along with the associated, reduced set of stochastic evolution equations. The transfo ... [Chaos 19, 043110 (2009)] published Thu Oct 29, 2009.
Self-assembly of polypeptides into left-handedly twisted fibril-like structures
Yan Mu and Yi Qin Gao
In this paper, we investigated the spontaneous formation of aggregation structures of amyloid-forming peptide (GGVVIA) using a coarse-grained model and Monte Carlo simulations. The effects of concentration and temperature on the formation of different aggregation structures were studied. Three types ... [Phys. Rev. E 80, 041927 (2009)] published Mon Oct 26, 2009.
Spectral solutions to stochastic models of gene expression with bursts and regulation
Andrew Mugler, Aleksandra M. Walczak, and Chris H. Wiggins
Signal-processing molecules inside cells are often present at low copy number, which necessitates probabilistic models to account for intrinsic noise. Probability distributions have traditionally been found using simulation-based approaches which then require estimating the distributions from many s ... [Phys. Rev. E 80, 041921 (2009)] published Tue Oct 20, 2009.
Rebuilding cytoskeleton roads: Active-transport-induced polarization of cells
R. J. Hawkins, O. Benichou, M. Piel, and R. Voituriez
Many cellular processes require a polarization axis which generally initially emerges as an inhomogeneous distribution of molecular markers in the cell. We present a simple analytical model of a general mechanism of cell polarization taking into account the positive feedback due to the coupled dynam ... [Phys. Rev. E 80, 040903 (2009)] published Mon Oct 19, 2009.
Cell adhesion: The effect of a surprising cohesive force
H. Vasseur
When an experimentalist or a biological mechanism applies an external force onto a cell chemically sticking to its substrate, a reacting suction force, due to the slow penetration of the surrounding fluid between the cell and the substrate, opposes to the dissociation. This force can overcome other ... [Phys. Rev. E 80, 042901 (2009)] published Fri Oct 9, 2009.
Maximum Likelihood and the Single Receptor
Robert G. Endres and Ned S. Wingreen
The accuracy by which biological cells sense chemical concentration is ultimately limited by the random arrival of particles at the receptors by diffusion. This fundamental physical limit is generally considered to be the Berg-Purcell limit [Biophys. J. 20, 193 (1977)]. Here we derive a lower limit ... [Phys. Rev. Lett. 103, 158101 (2009)] published Wed Oct 7, 2009.
Localized short impulses in a nerve model with self-excitable membrane
Alain M. Dikande and Ga-Akeku Bartholomew
During the generation and transmission of nerve impulses, the cytoplasm behaves like an excitable medium that self-regulates the shapes and magnitudes of the output excitation. In connection with this self-regulatory function, one can readily think of the plasma membrane as a nerve organ holding the ... [Phys. Rev. E 80, 041904 (2009)] published Mon Oct 5, 2009.
Evolutionary dynamics on rugged fitness landscapes: Exact dynamics and information theoretical aspects
David B. Saakian and Jose F. Fontanari
The parallel mutation-selection evolutionary dynamics, in which mutation and replication are independent events, is solved exactly in the case that the Malthusian fitnesses associated to the genomes are described by the random energy model (REM) and by a ferromagnetic version of the REM. The solutio ... [Phys. Rev. E 80, 041903 (2009)] published Fri Oct 2, 2009.
Compartmentalization of second messengers in neurons: A mathematical analysis
Wen Chen, Herbert Levine, and Wouter-Jan Rappel
Recent experiments in hippocampal neurons have demonstrated the existence of compartments with elevated levels of second messenger molecules such as cyclic AMP. This compartmentalization is believed to be necessary to ensure downstream signaling specificity. Here we use analytical and numerical tech ... [Phys. Rev. E 80, 041901 (2009)] published Fri Oct 2, 2009.
Thermodynamic Limit of a Nonequilibrium Steady State: Maxwell-Type Construction for a Bistable Biochemical System
Hao Ge and Hong Qian
We show that the thermodynamic limit of a bistable phosphorylation-dephosphorylation cycle has a selection rule for the more stable macroscopic steady state. The analysis is akin to the Maxwell construction. Based on the chemical master equation approach, it is shown that, except at a critical point ... [Phys. Rev. Lett. 103, 148103 (2009)] published Fri Oct 2, 2009.
Optimizing information flow in small genetic networks
Gasper TkaCik, Aleksandra M. Walczak, and William Bialek
In order to survive, reproduce, and (in multicellular organisms) differentiate, cells must control the concentrations of the myriad different proteins that are encoded in the genome. The precision of this control is limited by the inevitable randomness of individual molecular events. Here we explore ... [Phys. Rev. E 80, 031920 (2009)] published Tue Sep 29, 2009.
Harmonics and intermodulation in subthreshold FitzHughNagumo neuron
Wenjie Si, Jiang Wang, K. M. Tsang, and W. L. Chan
Intermodulation and harmonics are important in frequency analysis of nonlinear systems. In neuron research, most investigations are taken in studying synchronization between the external stimuli and the output of neuron, but harmonics and intermodulation are often ignored. In this paper, harmonics a ... [Chaos 19, 033144 (2009)] published Mon Sep 28, 2009.
DNA stretching and multivalent-cation-induced condensation
Yevgeni Sh. Mamasakhlisov, Brian A. Todd, Artem. V. Badasyan, Anna. V. Mkrtchyan, Vladimir. F. Morozov et al.
Motivated by measurements on stretched double-stranded DNA in the presence of multivalent cations, we develop a statistical mechanical model for the compaction of an insoluble semiflexible polymer under tension. Using a mean-field approach, we determine the order of the extended-to-compact transitio ... [Phys. Rev. E 80, 031915 (2009)] published Thu Sep 24, 2009.
Searching Fast for a Target on DNA without Falling to Traps
O. Benichou, Y. Kafri, M. Sheinman, and R. Voituriez
Genomic expression depends critically on both the ability of regulatory proteins to locate specific target sites on DNA within seconds and on the formation of long-lived (many minutes) complexes between these proteins and the DNA. Equilibrium experiments show that indeed regulatory proteins bind tig ... [Phys. Rev. Lett. 103, 138102 (2009)] published Thu Sep 24, 2009.
Effects of Jamming on Nonequilibrium Transport Times in Nanochannels
A. Zilman, J. Pearson, and G. Bel
Many biological channels perform highly selective transport without direct input of metabolic energy and without transitions from a closed to an open state during transport. Mechanisms of selectivity of such channels serve as an inspiration for creation of artificial nanomolecular sorting devices an ... [Phys. Rev. Lett. 103, 128103 (2009)] published Thu Sep 17, 2009.
A Mathematical Model of Antiretroviral Therapy Evaluation for HIV Type 1
Silvia Martorano Raimundo, Ezio Venturino, and Hyun Mo Yang
Treating HIV-infected patients with a combination of several antiretroviral drugs can lead to emergence of the drug-resistant strain. This work proposes a mathematical model to evaluate the emergence of HIV-1 drug resistant during antiretroviral therapy. The model assumes that all susceptible indivi ... [AIP Conf. Proc. 1168, 1552 (2009)] published Mon Sep 14, 2009.
lambda-prophage induction modeled as a cooperative failure mode of lytic repression
Nicholas Chia, Ido Golding, and Nigel Goldenfeld
We analyze a system-level model for lytic repression of lambda phage in E. coli using reliability theory, showing that the repressor circuit comprises four redundant components whose failure mode is prophage induction. Our model reflects the specific biochemical mechanisms involved in regulation, in ... [Phys. Rev. E 80, 030901 (2009)] published Tue Sep 1, 2009.
Solutions to the Michaelis-Menten Kinetics are not Necessarily Unique
Karl-Ernst Biebler, Kristine Schreiber, and Rudiger Bode
The classic enzyme substratum reaction is described by a nonlinear system of four differential equations. The related initial value problem does not have an explicit solution. Steady-state assumptions lead to the well known Michaelis-Menten kinetics. They are approximations of the solutions of the o ... [AIP Conf. Proc. 1148, 37 (2009)] published Mon Aug 24, 2009.
Advantages and Disadvantages of Double Threaded Dental Implant Screws As Opposed to Single-Threaded: A Study from a Biomechanical Perspective by the Finite Element Method
A. Alvarez-Arenal, F. J. de Cos Juez, F. Sanchez Lasheras, and M. Mauvezin Quevedo
The purpose of the present article is to study the advantages from a biomechanical point of view of the use of a double-threaded dental implant over the more common single-threaded one. For this purpose a 3D model of a portion of the jaw was generated. In this model four different bone areas were di ... [AIP Conf. Proc. 1148, 13 (2009)] published Mon Aug 24, 2009.
A docking analysis of the statistical physics of protein–protein recognition
IOP http://syndication.iop.org
Min-oscillations in Escherichia coli induced by interactions of membrane-bound proteins
IOP http://syndication.iop.org
Environmental selection of the feed-forward loop circuit in gene-regulation networks
IOP http://syndication.iop.org
Protein–protein interactions: principles and predictions
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Prediction of physical protein–protein interactions
IOP http://syndication.iop.org
Modeling tubular shapes in the inner mitochondrial membrane
IOP http://syndication.iop.org
Tracking single particles: a user-friendly quantitative evaluation
IOP http://syndication.iop.org
Reactive clusters on a membrane
IOP http://syndication.iop.org
Monte Carlo simulation of bifurcation in the intracellular viral kinetics
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Noise characteristics of feed forward loops
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