Virtual Journal of Biological Physics Research

Inkjet delivery of glucose oxidase

Christopher C. Cook, Tianming Wang, and Brian Derby
The activity of glucose oxidase is reduced by inkjet printing and is a function of the printing conditions. Standard characterisation methods show no significant change to enzyme molecular weight, secondary structure and general molecular shape as a function of printing parameters. This indicates th ... [Chem. Commun. 46, 5452 (2010)] published Mon Jul 26, 2010.

Two-Dimensional Raman Correlation Analysis of Diseased Esophagus in a Rat

Sota Takanezawa, Shin-ichi Morita, Atsushi Maruyama, Takurou N. Murakami, Norimichi Kawashima et al.
Generalized two-dimensional (2D) Raman correlation analysis effectively distinguished a benign tumor from normal tissue. Line profiling Raman spectra of a rat esophagus, including a benign tumor, were measured and the generalized 2D synchronous and asynchronous spectra were calculated. In the autoco ... [Appl. Phys. Express 3, 077001 (2010)] published Mon Jul 26, 2010.

Cell transfection using layer-by-layer (LbL) coated calixarene-based solid lipid nanoparticles (SLNs)

Laurent Nault, Alessandro Cumbo, Rene F. Pretot, Michel A. Sciotti, and Patrick Shahgaldian
Polycationic calixarene-based solid lipid nanoparticles (SLNs) have been loaded at their surface with DNA and chitosan and studied for their ability to transfect mammalian cells. ... [Chem. Commun. 46, 5581 (2010)] published Mon Jul 26, 2010.

Self-aggregation of oligonucleotide-functionalized gold nanoparticles and its applications for highly sensitive detection of DNA

Jinzhao Song, Zhengping Li, Yongqiang Cheng, and Chenghui Liu
A new self-aggregation phenomenon of single strand DNA-modified gold nanoparticles has been demonstrated and applied to highly sensitive DNA detection. ... [Chem. Commun. 46, 5548 (2010)] published Mon Jul 26, 2010.

Molecular Recognition in the Digital Radio Domain

William D. Hunt, Peter J. Edmonson, Desmond D. Stubbs, and Sang-Hun Lee
In this paper we discuss the theoretical and experimental constructs which together point the way towards the transduction of biomolecular recognition events into a palpable set of electrical signals. This combines the applied physics of surface perturbations on acoustic wave device surfaces and ... [Jpn. J. Appl. Phys. 49, 07HA02 (2010)] published Mon Jul 26, 2010.

Dendrimer porphyrin-terminated polyelectrolyte multilayer micropatterns for a protein microarray with enhanced sensitivity

Kyung Jin Son, Suhyun Kim, Joo-Ho Kim, Woo-Dong Jang, Yeol Lee et al.
Through a combination of layer-by-layer (LbL) self-assembly (SA) and lift-off methods, a dendrimer-coated polyelectrolyte multilayer micropattern was prepared for protein microarrays. A silicon substrate was patterned with a photoresist thin film using conventional photolithography, and then poly(et ... [J. Mater. Chem. 20, 6531 (2010)] published Wed Jul 28, 2010.

Predictive modeling of lung motion over the entire respiratory cycle using measured pressure-volume data, 4DCT images, and finite-element analysis

Jaesung Eom, Xie George Xu, Suvranu De, and Chengyu Shi
Purpose: Predicting complex patterns of respiration can benefit the management of the respiratory motion for radiation therapy of lung cancer. The purpose of the present work was to develop a patient-specific, physiologically relevant respiratory motion model which is capable of predicting lung tumo ... [Med. Phys. 37, 4389 (2010)] published Wed Jul 28, 2010.

Vortex-assisted DNA delivery

Jun Wang, Yihong Zhan, Victor M. Ugaz, and Chang Lu
Electroporation is one of the most widely used methods to deliver exogenous DNA payloads into cells, but a major limitation is that only a small fraction of the total membrane surface is permeabilized. Here we show how this barrier can be easily overcome by harnessing hydrodynamic effects associated ... [Lab Chip 10, 2057 (2010)] published Wed Jul 28, 2010.

Real-time, step-wise, electrical detection of protein molecules using dielectrophoretically aligned SWNT-film FET aptasensors

Taechang An, Ki Su Kim, Sei Kwang Hahn, and Geunbae Lim
Aptamer functionalized addressable SWNT-film arrays between cantilever electrodes were successfully developed for biosensor applications. Dielectrophoretically aligned SWNT suspended films made possible highly specific and rapid detection of target proteins with a large binding surface area. Thrombi ... [Lab Chip 10, 2052 (2010)] published Wed Jul 28, 2010.

Effect of ultrasound transducer face reflectivity on the light fluence inside a turbid medium in photoacoustic imaging

Behnoosh Tavakoli, Patrick D. Kumavor, Andres Aguirre, and Quing Zhu
Many endoscopic, intravascular, and transvaginal applications require light to be delivered through optical fibers in a reflection mode. For photoacoustic imaging in reflection geometry, the front-face reflectivity of the ultrasound transducer face imposes a boundary condition that affects the light ... [J. Biomed. Opt. 15, 046003 (2010)] published Tue Jul 20, 2010.

Stacked graphene nanofibers for electrochemical oxidation of DNA bases

Adriano Ambrosi and Martin Pumera
In this article, we show that stacked graphene nanofibers (SGNFs) demonstrate superior electrochemical performance for oxidation of DNA bases over carbon nanotubes (CNTs). This is due to an exceptionally high number of accessible graphene sheet edges on the surface of the nanofibers when compared to ... [Phys. Chem. Chem. Phys. 12, 8943 (2010)] published Thu Jul 29, 2010.

On the use of a proton path probability map for proton computed tomography reconstruction

Dongxu Wang, T. Rockwell Mackie, and Wolfgang A. Tome
Purpose: To describe a method to estimate the proton path in proton computed tomography (pCT) reconstruction, which is based on the probability of a proton passing through each point within an object to be imaged.Methods: Based on multiple Coulomb scattering and a semianalytically derived model, the ... [Med. Phys. 37, 4138 (2010)] published Tue Jul 20, 2010.

Magnet polepiece design for uniform magnetic force on superparamagnetic beads

Todd Fallesen, David B. Hill, Matthew Steen, Jed C. Macosko, Keith Bonin et al.
Here we report construction of a simple electromagnet with novel polepieces which apply a spatially uniform force to superparamagnetic beads in an optical microscope. The wedge-shaped gap was designed to keep [partial-derivative]B/[partial-derivative]y constant and B large enough to saturate the bea ... [Rev. Sci. Instrum. 81, 074303 (2010)] published Thu Jul 29, 2010.

Development of a multitarget tracking system for paramecia

Yu-Sing Yeh, Ke-Nung Huang, Sun-Lon Jen, Yan-Chay Li, and Ming-Shing Young
This investigation develops a multitarget tracking system for the motile protozoa, paramecium. The system can recognize, track, and record the orbit of swimming paramecia within a 4 mm diameter of a circular experimental pool. The proposed system is implemented using an optical microscope, a charge- ... [Rev. Sci. Instrum. 81, 074302 (2010)] published Wed Jul 21, 2010.

Development of 170 MHz Electrodeless Quartz-Crystal Microbalance Immunosensor with Nonspecifically Immobilized Receptor Proteins

Hirotsugu Ogi, Hironao Nagai, Yuji Fukunishi, Taiji Yanagida, Masahiko Hirao et al.
Staphylococcus aureus protein A (SPA) shows high nonspecific binding affinity on a naked quartz surface, and it can be used as the receptor protein for detecting immunoglobulin G (IgG), the most important immunoglobulin. The immunosensor ability, however, significantly depends on the immobilizat ... [Jpn. J. Appl. Phys. 49, 07HD07 (2010)] published Mon Jul 26, 2010.

Note: Microelectromechanical systems Coulter counter for cell monitoring and counting

Yifan Wu, James D. Benson, John K. Critser, and Mahmoud Almasri
This note describes the design, fabrication, and testing of a novel microelectromechanical systems Coulter counter. The Coulter counter will be used to detect and monitor impedance changes of cells as a function of time in response to different experimental extracellular environments. The device con ... [Rev. Sci. Instrum. 81, 076103 (2010)] published Mon Jul 19, 2010.

Two-dimensional dielectric spectroscopy: Implementation and validation of a scanning open-ended coaxial probe

Mohammad Habibi, David P. Klemer, and Valerica Raicu
Dielectric spectroscopy is a powerful tool for characterizing and classifying materials based on their electrical properties. In order to perform dielectric measurements on a sample with spatially varying properties, the measuring probe typically is repositioned manually on the surface of the sample ... [Rev. Sci. Instrum. 81, 075108 (2010)] published Fri Jul 23, 2010.

Giant magnetoimpedance-based microchannel system for quick and parallel genotyping of human papilloma virus type 16/18

Hao Yang, Lei Chen, Chong Lei, Ju Zhang, Ding Li et al.
Quick and parallel genotyping of human papilloma virus (HPV) type 16/18 is carried out by a specially designed giant magnetoimpedance (GMI) based microchannel system. Micropatterned soft magnetic ribbon exhibiting large GMI ratio serves as the biosensor element. HPV genotyping can be determined by t ... [Appl. Phys. Lett. 97, 043702 (2010)] published Mon Jul 26, 2010.

Three-dimensional flexible microprobe for recording the neural signal

Chang-Hsiao Chen, Shih-Chang Chuang, Yu-Tao Lee, Yen-Chung Chang, Shih-Rung Yeh et al.
We have designed, fabricated, and tested a novel three-dimensional (3-D) flexible microprobe used for recording the neural signals of lateral giant (LG) on the escape system of American crayfish. We report an electrostatic actuation process to fold the planar probes to be the arbitrary orientations ... [J. Micro/Nanolith. MEMS MOEMS 9, 031007 (2010)] published Fri Jul 23, 2010.

Near-infrared Raman spectroscopy to detect anti-Toxoplasma gondii antibody in blood sera of domestic cats: quantitative analysis based on partial least-squares multivariate statistics

Janaina Duarte, Marcos T. T. Pacheco, Antonio Balbin Villaverde, Rosangela Z. Machado, Renato A. Zangaro et al.
Toxoplasmosis is an important zoonosis in public health because domestic cats are the main agents responsible for the transmission of this disease in Brazil. We investigate a method for diagnosing toxoplasmosis based on Raman spectroscopy. Dispersive near-infrared Raman spectra are used to quantify ... [J. Biomed. Opt. 15, 047002 (2010)] published Wed Jul 21, 2010.

Alterations in the characteristic size distributions of subcellular scatterers at the onset of apoptosis: effect of Bcl-x and Bax/Bak

Jing-Yi Zheng and Nada N. Boustany
Optical scatter imaging is used to estimate organelle size distributions in immortalized baby mouse kidney cells treated with 0.4 [mu]M staurosporine to induce apoptosis. The study comprises apoptosis competent iBMK cells (W2) expressing the proapoptotic proteins Bax/Bak, apoptosis resistant Bax/Ba ... [J. Biomed. Opt. 15, 045002 (2010)] published Fri Jul 16, 2010.

Needle-compatible single fiber bundle image guide reflectance endoscope

Jiantang Sun, Chenghao Shu, Benjamin Appiah, and Rebekah Drezek
We developed a miniaturized high-resolution low-cost reflectance-mode fiber microscope (RFM) aimed at optical tissue biopsy applications using a polarized imaging configuration to suppress background noise from specular reflectance. The RFM is equipped with an air-cooled light-emitting-diode illumin ... [J. Biomed. Opt. 15, 040502 (2010)] published Thu Jul 29, 2010.

The Sonochemical and Biological Effects of Three Clinically-Used Contrast Agents

Mariame A. Hassan, Loreto B. Feril, Nobuki Kudo, Katsuro Tachibana, Takashi Kondo et al.
The encapsulation of gas bubbles has resulted in improved stability and added a binding capacity to shells for ultrasound-guided targeted delivery. However, this has also changed the physical and acoustical properties of the final formulation. In this study, we have evaluated three clinically-us ... [Jpn. J. Appl. Phys. 49, 07HF23 (2010)] published Mon Jul 26, 2010.

Fast three dimensional ac electro-osmotic pumps with nonphotolithographic electrode patterning

Y. M. Senousy and C. K. Harnett
Three dimensional (3D) stepped electrodes dramatically improve the flow rate and frequency range of ac electro-osmotic pumps, compared to planar electrodes. However, the fabrication of 3D stepped electrodes for ac electro-osmosis (ACEO) pumps usually involves several processing steps. This paper dem ... [Biomicrofluidics 4, 036501 (2010)] published Fri Jul 16, 2010.

Impedance spectroscopy on stretchable microelectrode arrays

I. R. Minev and S. P. Lacour
We are reporting on the fabrication and electrical characterization of stretchable polydimethylsiloxane (PDMS) based microelectrode arrays for recording of neuronal action potentials. Electrodes are immersed in phosphate buffered saline solution. Their electrical impedance spectra are recorded as a ... [Appl. Phys. Lett. 97, 043707 (2010)] published Thu Jul 29, 2010.

Egg white as a blood coagulation surrogate

Yunbo Liu, Subha Maruvada, Bruce A. Herman, and Gerald R. Harris
Egg white, a protein-containing solution, is characterized as a blood coagulation surrogate for the acoustical and thermal evaluation of therapeutic ultrasound, especially high intensity focused ultrasound (HIFU) devices. Physical properties, including coagulation temperature, frequency dependent at ... [J. Acoust. Soc. Am. 128, 480 (2010)] published Fri Jul 16, 2010.

New methodology to assess activity status of occlusal caries in primary teeth using laser fluorescence device

Mariana Minatel Braga, Monique Saveriano de Benedetto, Jose Carlos Pettorossi Imparato, and Fausto Medeiros Mendes
An in vivo study was conducted to verify the ability of laser fluorescence (LF) to assess the activity status of occlusal caries in primary teeth, using different air-drying times. Occlusal sites (707) were examined using LF (DIAGNOdent) after air-drying for 3 s and 15 s, and the difference betwee ... [J. Biomed. Opt. 15, 047005 (2010)] published Thu Jul 29, 2010.

Microfluidic dissolved oxygen gradient generator biochip as a useful tool in bacterial biofilm studies

Maciej Skolimowski, Martin Weiss Nielsen, Jenny Emneus, Soren Molin, Rafael Taboryski et al.
A microfluidic chip for generation of gradients of dissolved oxygen was designed, fabricated and tested. The novel way of active oxygen depletion through a gas permeable membrane was applied. Numerical simulations for generation of O gradients were correlated with measured oxygen concentrations. The ... [Lab Chip 10, 2162 (2010)] published Wed Jul 28, 2010.

In situ mechanical characterization of mouse oocytes using a cell holding device

Xinyu Liu, Roxanne Fernandes, Andrea Jurisicova, Robert F. Casper, and Yu Sun
This paper presents a cellular force measurement technique that allows for mechanical characterization of mouse oocytes during microinjection (i.e., in situ) without requiring a separate characterization process. The technique employs an elastic cell holding device and a sub-pixel computer vision tr ... [Lab Chip 10, 2154 (2010)] published Wed Jul 28, 2010.

Fiber-optic multiphoton flow cytometry in whole blood and in vivo

Yu-Chung Chang, Jing Yong Ye, Thommey P. Thomas, Zhengyi Cao, Alina Kotlyar et al.
Circulating tumor cells in the bloodstream are sensitive indicators for metastasis and disease prognosis. Circulating cells have usually been monitored via extraction from blood, and more recently in vivo using free-space optics; however, long-term intravital monitoring of rare circulating cells rem ... [J. Biomed. Opt. 15, 047004 (2010)] published Mon Jul 26, 2010.

Blood Flow Measurement by the Counter-Crossed Beam Contrast Echo Method

Taishi Eura, Kenji Yoshida, Yoshiaki Watanabe, and Iwaki Akiyama
We propose a new contrast-echo method using the counter-crossed beams of two ultrasonic frequencies for ultrasound diagnosis of cancer and call it the counter-cross beam contrast echo (C-CBCE) method. In this C-CBCE method, the sum- or difference-frequency components generated by the nonlinear v ... [Jpn. J. Appl. Phys. 49, 07HF05 (2010)] published Mon Jul 26, 2010.

Application of electroosmotically-driven solution displacement for on-chip probing and characterization of protein adsorption

Szu-Wei Tang, Chien-Hsiang Chang, and Hsien-Hung Wei
An alternative strategy for realizing on-chip characterization of protein adsorption is demonstrated using solution displacement with electro-osmotic flow in microchannels. The idea is illustrated by studying adsorption of bovine serum albumin (BSA) on polydimethylsiloxane surfaces. Through tracking ... [Appl. Phys. Lett. 97, 043704 (2010)] published Wed Jul 28, 2010.

Gold nanoparticles: dispersibility in biological media and cell-biological effect

Dirk Mahl, Christina Greulich, Wolfgang Meyer-Zaika, Manfred Koller, and Matthias Epple
Spherical gold nanoparticles with a hydrodynamic diameter between 25 and 37 nm were prepared and stabilised with poly(N-vinylpyrrolidone) (PVP) or tris(sodium-m-sulfonatophenyl)phosphine (TPPTS). They were subjected to different cell culture media, e.g. pure RPMI, RPMI containing up to 10% of fetal ... [J. Mater. Chem. 20, 6176 (2010)] published Mon Jul 26, 2010.

Integration of plasma-assisted surface chemical modification, soft lithography, and protein surface activation for single-cell patterning

Q. Cheng and K. Komvopoulos
Surface patterning for single-cell culture was accomplished by combining plasma-assisted surface chemical modification, soft lithography, and protein-induced surface activation. Hydrophilic patterns were produced on Parylene C films deposited on glass substrates by oxygen plasma treatment through th ... [Appl. Phys. Lett. 97, 043705 (2010)] published Wed Jul 28, 2010.

Carbon Paste Gold Nanoparticles Sensor for the Selective Determination of Dopamine in Buffered Solutions

Nada F. Atta, Ahmed Galal, Fekria M. Abu-Attia, and Shereen M. Azab
An effective electrochemical sensor for the selective determination of dopamine (DA) in the presence of ascorbic acid (AA) and uric acid (UA) in 0.04 mol L universal buffer solution (pH 7.4) is introduced. The sensor is based on a carbon paste (CP) electrode modified with gold nanoparticles. In a ... [J. Electrochem. Soc. 157, F116 (2010)] published Fri Jul 16, 2010.

Chemical stimulation of the Arabidopsis thaliana root using multi-laminar flow on a microfluidic chip

Matthias Meier, Elena M. Lucchetta, and Rustem F. Ismagilov
In this article, we developed a plant on a chip microfluidic platform that can control the local chemical environment around live roots of Arabidopsis thaliana with high spatial resolution using multi-laminar flow. We characterized the flow profile around the Arabidopsis root, and verified that the ... [Lab Chip 10, 2147 (2010)] published Wed Jul 28, 2010.

Quantum-dot/dopamine bioconjugates function as redox coupled assemblies for in vitro and intracellular pH sensing

Igor L. Medintz, Michael H. Stewart, Scott A. Trammell, Kimihiro Susumu, James B. Delehanty et al.
The use of semiconductor quantum dots (QDs) for bioimaging and sensing has progressively matured over the past decade. QDs are highly sensitive to charge-transfer processes, which can alter their optical properties. Here, we demonstrate that QDdopaminepeptide bioconjugates can function as charge-tra ... [Nature Mater. 9, 676 (2010)] published Mon Jul 26, 2010.

Mechanistic formulation of a lineal-quadratic-linear (LQL) model: Split-dose experiments and exponentially decaying sources

Mariana Guerrero and Marco Carlone
Purpose: In recent years, several models were proposed that modify the standard linear-quadratic (LQ) model to make the predicted survival curve linear at high doses. Most of these models are purely phenomenological and can only be applied in the particular case of acute doses per fraction. The auth ... [Med. Phys. 37, 4173 (2010)] published Tue Jul 20, 2010.

Lab-on-a-chip devices as an emerging platform for stem cell biology

Kshitiz Gupta, Deok-Ho Kim, David Ellison, Christopher Smith, Arnab Kundu et al.
The advent of stem cell based therapies has brought regenerative medicine into an increased focus as a part of the modern medicine practice, with a potential to treat a myriad of intractable diseases in the future. Stem cells reside in a complex microenvironment presenting them with a multitude of p ... [Lab Chip 10, 2019 (2010)] published Wed Jul 28, 2010.

Development of trifunctional probes for glycoproteomic analysis

Charng-Sheng Tsai, Po-Yu Liu, Hsin-Yung Yen, Tsui-Ling Hsu, and Chi-Huey Wong
A new trifunctional probe, assembled using a cleavable linker, is useful for efficient enrichment and detection of alkynyl sugar-tagged biomolecules. ... [Chem. Commun. 46, 5575 (2010)] published Mon Jul 26, 2010.

One-step extraction of subcellular proteins from eukaryotic cells

Yihong Zhan, Victoria A. Martin, Robert L. Geahlen, and Chang Lu
Conventional biochemical analysis mainly focuses on the expression level of cellular proteins from entire cells. However, it has been increasingly acknowledged that the subcellular location of proteins often carries important information. Analysis of subcellular proteins conventionally requires subc ... [Lab Chip 10, 2046 (2010)] published Wed Jul 28, 2010.

Differential conductance as a promising approach for rapid DNA sequencing with nanopore-embedded electrodes

Yuhui He, Lubing Shao, Ralph H. Scheicher, Anton Grigoriev, Rajeev Ahuja et al.
We propose an approach for nanopore-based DNA sequencing using characteristic transverse differential conductance. Molecular dynamics and electron transport simulations show that the transverse differential conductance during the translocation of DNA through the nanopore is distinguishable enough fo ... [Appl. Phys. Lett. 97, 043701 (2010)] published Mon Jul 26, 2010.

Photoacoustic lifetime imaging of dissolved oxygen using methylene blue

Shai Ashkenazi
Measuring distribution of dissolved oxygen in biological tissue is of prime interest for cancer diagnosis, prognosis, and therapy optimization. Tumor hypoxia indicates poor prognosis and resistance to radiotherapy. Despite its major clinical significance, no current imaging modality provides direct ... [J. Biomed. Opt. 15, 040501 (2010)] published Wed Jul 21, 2010.

High voltage-derived enhancement of electric conduction in nanogap devices for detection of prostate-specific antigen

Hyung Ju Park, Young Shik Chi, Insung S. Choi, and Wan Soo Yun
We report a simple method of enhancing electric conductance in nanogap devices without any additional treatments, such as silver-enhancing process. The low electric conductance after selective immobilization of biofunctionalized gold nanoparticles in the gap region was greatly enhanced by repeated I ... [Appl. Phys. Lett. 97, 033701 (2010)] published Tue Jul 20, 2010.

Gigaohm resistance membrane seals with stealth probe electrodes

Piyush Verma and Nicholas A. Melosh
Direct electrical access into the cell interior is required for low-noise recording of ion channel activity, yet conventional patch clamp techniques are destructive, leading to rapid cell death, while on-chip devices have poor seal resistances. Here we report chip-based nanoscale electrodes that non ... [Appl. Phys. Lett. 97, 033704 (2010)] published Wed Jul 21, 2010.

Comparison of absorbed fractions of electrons and photons using three kinds of computational phantoms of rat

Tianwu Xie, Guozhi Zhang, Yun Li, and Qian Liu
Rats have been widely used in radiopharmaceutics researches, making it reasonable to develop fine structured computational models for rat internal dose investigation. In this work, we developed three existing types of computational phantoms based on the same data set of rat, simulated photon and ele ... [Appl. Phys. Lett. 97, 033702 (2010)] published Tue Jul 20, 2010.

Plasmon-enhanced microalgal growth in miniphotobioreactors

S. Torkamani, S. N. Wani, Y. J. Tang, and R. Sureshkumar
Photoactivity of green microalgae is nonmonotonic across the electromagnetic spectrum. Experiments on Chlamydomonas reinhardtii (green alga) and Cyanothece 51142 (green-blue alga) show that wavelength specific backscattering in the blue region of the spectrum from Ag nanoparticles, caused by localiz ... [Appl. Phys. Lett. 97, 043703 (2010)] published Tue Jul 27, 2010.

A harmonic transition state approximation for the duration of reactive events in complex molecular rearrangements

Srabanti Chaudhury and Dmitrii E. Makarov
Motivated by recent experimental efforts to measure the time a molecular system spends in transit between the reactants and the products of a chemical reaction, here we study the properties of the distribution of such transit times for the case of conservative dynamics on a multidimensional energy l ... [J. Chem. Phys. 133, 034118 (2010)] published Tue Jul 20, 2010.

Inference in alpha rhythm phase and amplitude modeled on Markov random field using belief propagation from electroencephalograms

Yasushi Naruse, Ken Takiyama, Masato Okada, and Tsutomu Murata
Alpha rhythm is a major component of spontaneous electroencephalographic (EEG) data. We develop a novel method that can be used to estimate the instantaneous phases and amplitudes of the alpha rhythm with high accuracy by modeling the alpha rhythm phase and amplitude as Markov random field (MRF) mod ... [Phys. Rev. E 82, 011912 ] published .

Analytic expression for the mean time to absorption for a random walker on the Sierpinski gasket. II. The eigenvalue spectrum

Jonathan L. Bentz, John W. Turner, and John J. Kozak
We continue the study of a particle (atom, molecule) undergoing an unbiased random walk on the Sierpinski gasket, and obtain for the gasket and tower the eigenvalue spectrum of the associated stochastic master equation. Analytic expressions for recurrence relations among the eigenvalues are derived. ... [Phys. Rev. E 82, 011137 ] published .

Extinction of refugia of hantavirus infection in a spatially heterogeneous environment

Niraj Kumar, R. R. Parmenter, and V. M. Kenkre
We predict an abrupt observable transition, on the basis of numerical studies, of hantavirus infection in terrain characterized by spatially dependent environmental resources. The underlying framework of the analysis is that of Fisher equations with an internal degree of freedom, the state of infect ... [Phys. Rev. E 82, 011920 ] published .

Comment on Dynamical phase transition of a one-dimensional transport process including death

H. W. Kwon and M. Y. Choi
Motivated by the mycologic situation, Dorosz and collaborators considered a modification of the totally asymmetric exclusion process, including the probabilities of injection and of death. In the case of the backward-ordered sequential dynamics with the death probability larger than the critical val ... [Phys. Rev. E 82, 013101 ] published .

Complex intermittency blurred by noise: Theory and application to neural dynamics

Paolo Allegrini, Danilo Menicucci, Remo Bedini, Angelo Gemignani, and Paolo Paradisi
We propose a model for the passage between metastable states of mind dynamics. As changing points we use the rapid transition processes simultaneously detectable in EEG signals related to different cortical areas. Our model consists of a non-Poissonian intermittent process, which signals that the br ... [Phys. Rev. E 82, 015103 ] published .

Effects of mass media action on the Axelrod model with social influence

Arezky H. Rodriguez and Y. Moreno
The use of dyadic interaction between agents, in combination with homophily (the principle that likes attract) in the Axelrod model for the study of cultural dissemination, has two important problems: the prediction of monoculture in large societies and an extremely narrow window of noise levels in ... [Phys. Rev. E 82, 016111 ] published .

Statistics of camera-based single-particle tracking

Andrew J. Berglund
Camera-based single-particle tracking enables quantitative determination of transport properties and provides nanoscale information about material characteristics such as viscosity and elasticity. However, static localization noise and the blurring of a particle's position over camera integration ti ... [Phys. Rev. E 82, 011917 ] published .

Quantifying chaos for ecological stoichiometry

Jorge Duarte, Cristina Januario, Nuno Martins, and Josep Sardanyes
The theory of ecological stoichiometry considers ecological interactions among species with different chemical compositions. Both experimental and theoretical investigations have shown the importance of species composition in the outcome of the population dynamics. A recent study of a theoretical th ... [Chaos 20, 033105 (2010)] published Fri Jul 23, 2010.

Maximum caliber inference of nonequilibrium processes

Moritz Otten and Gerhard Stock
Thirty years ago, Jaynes suggested a general theoretical approach to nonequilibrium statistical mechanics, called maximum caliber (MaxCal) [Annu. Rev. Phys. Chem. 31, 579 (1980)]. MaxCal is a variational principle for dynamics in the same spirit that maximum entropy is a variational principle for eq ... [J. Chem. Phys. 133, 034119 (2010)] published Wed Jul 21, 2010.

Generalized-Ensemble Algorithms for the IsobaricIsothermal Ensemble

Yoshiharu Mori and Yuko Okamoto
We present generalized-ensemble algorithms for isobaricisothermal molecular simulations. In addition to the multibaricmultithermal algorithm and replica-exchange method for the isobaricisothermal ensemble, which have already been proposed, we propose a simulated tempering method for this ensembl ... [J. Phys. Soc. Jpn. 79, 074003 (2010)] published Mon Jul 26, 2010.

An efficient umbrella potential for the accurate calculation of free energies by molecular simulation

Di Wu
Umbrella sampling has been widely used to calculate free energies in many chemical and biological applications because it can effectively bridge the systems of interest and sample in the united phase space that is essential to yield accurate results. Many algorithms have implemented the idea of umbr ... [J. Chem. Phys. 133, 044115 (2010)] published Thu Jul 29, 2010.

Quasi-Newton parallel geometry optimization methods

Steven K. Burger and Paul W. Ayers
Algorithms for parallel unconstrained minimization of molecular systems are examined. The overall framework of minimization is the same except for the choice of directions for updating the quasi-Newton Hessian. Ideally these directions are chosen so the updated Hessian gives steps that are same as u ... [J. Chem. Phys. 133, 034116 (2010)] published Tue Jul 20, 2010.

Population distribution of flexible molecules from maximum entropy analysis using different priors as background information: application to the [cursive phi], psi-conformational space of the alpha-(1-->2)-linked mannose disaccharide present in N- and O-linked glycoproteins

Elin Sawen, Tariq Massad, Clas Landersjo, Peter Damberg, and Goran Widmalm
The conformational space available to the flexible molecule alpha-d-Manp-(1-->2)-alpha-d-Manp-OMe, a model for the alpha-(1-->2)-linked mannose disaccharide in N- or O-linked glycoproteins, is determined using experimental data and molecular simulation combined with a maximum entropy approach that l ... [Org. Biomol. Chem. 8, 3684 (2010)] published Thu Jul 29, 2010.

Spatial averaging for small molecule diffusion in condensed phase environments

Nuria Plattner, J. D. Doll, and Markus Meuwly
Spatial averaging is a new approach for sampling rare-event problems. The approach modifies the importance function which improves the sampling efficiency while keeping a defined relation to the original statistical distribution. In this work, spatial averaging is applied to multidimensional systems ... [J. Chem. Phys. 133, 044506 (2010)] published Mon Jul 26, 2010.

An effective rate equation approach to reaction kinetics in small volumes: Theory and application to biochemical reactions in nonequilibrium steady-state conditions

R. Grima
Chemical master equations provide a mathematical description of stochastic reaction kinetics in well-mixed conditions. They are a valid description over length scales that are larger than the reactive mean free path and thus describe kinetics in compartments of mesoscopic and macroscopic dimensions. ... [J. Chem. Phys. 133, 035101 (2010)] published Fri Jul 16, 2010.

Subdiffusive motion of a polymer composed of subdiffusive monomers

Stephanie C. Weber, Julie A. Theriot, and Andrew J. Spakowitz
We use Brownian dynamics simulations and analytical theory to investigate the physical principles underlying subdiffusive motion of a polymer. Specifically, we examine the consequences of confinement, self-interaction, viscoelasticity, and random waiting on monomer motion, as these physical phenomen ... [Phys. Rev. E 82, 011913 ] published .

Ergodic directional switching in mobile insect groups

Carlos Escudero, Christian A. Yates, Jerome Buhl, Iain D. Couzin, Radek Erban et al.
We obtain a Fokker-Planck equation describing experimental data on the collective motion of locusts. The noise is of internal origin and due to the discrete character and finite number of constituents of the swarm. The stationary probability distribution shows a rich phenomenology including nonmonot ... [Phys. Rev. E 82, 011926 ] published .

Origin of a function by tandem gene duplication limits the evolutionary capability of its sister copy

Martin Hasselmann, Sarah Lechner, Christina Schulte, and Martin Beye
The most remarkable outcome of a gene duplication event is the evolution of a novel function. Little information exists on how the rise of a novel function affects the evolution of its paralogous sister gene copy, however. We studied the evolution of the feminizer (fem) gene from which the gene com ... [Proc. Natl. Acad. Sci. U.S.A. 107, 13378 (2010)] published Wed Jul 28, 2010.

Stochastic slowdown in evolutionary processes

Philipp M. Altrock, Chaitanya S. Gokhale, and Arne Traulsen
We examine birth-death processes with state dependent transition probabilities and at least one absorbing boundary. In evolution, this describes selection acting on two different types in a finite population where reproductive events occur successively. If the two types have equal fitness the system ... [Phys. Rev. E 82, 011925 ] published .

Marginally Stable Chemical Systems as Precursors of Life

Doriano Brogioli
Current research on the origin of life aims at finding the simplest entity that can undergo spontaneous Darwinian evolution toward increasing replication efficiency. Here I consider some of the models of self-replicating molecular systems, and I show that they exhibit a distinct feature, namely, an ... [Phys. Rev. Lett. 105, 058102 ] published .

Early Chordate Origins of the Vertebrate Second Heart Field

Alberto Stolfi, T. Blair Gainous, John J. Young, Alessandro Mori, Michael Levine et al.
The vertebrate heart is formed from diverse embryonic territories, including the first and second heart fields. The second heart field (SHF) gives rise to the right ventricle and outflow tract, yet its evolutionary origins are unclear. We found that heart progenitor cells of the simple chordate Cion ... [Science 329, 565 ] published .

Individual histories and selection in heterogeneous populations

Stanislas Leibler and Edo Kussell
The strength of selection in populations has traditionally been inferred by measuring changes in bulk population parameters, such as mean reproductive rates. Untangling the effect of selection from other factors, such as specific responses to environmental fluctuations, poses a significant problem ... [Proc. Natl. Acad. Sci. U.S.A. 107, 13183 (2010)] published Mon Jul 26, 2010.

DNA polymerase {theta} up-regulation is associated with poor survival in breast cancer, perturbs DNA replication, and promotes genetic instability

Fanny Lemee, Valerie Bergoglio, Anne Fernandez-Vidal, Alice Machado-Silva, Marie-Jeanne Pillaire et al.
"Replicative stress" is one of the main factors underlying neoplasia from its early stages. Genes involved in DNA synthesis may therefore represent an underexplored source of potential prognostic markers for cancer. To this aim, we generated gene expression profiles from two independent cohorts (Fr ... [Proc. Natl. Acad. Sci. U.S.A. 107, 13390 (2010)] published Wed Jul 28, 2010.

Hairpin DNA coated gold nanoparticles as intracellular mRNA probes for the detection of tyrosinase gene expression in melanoma cells

S. Reese Harry, Donna J. Hicks, Katayoun I. Amiri, and David W. Wright
A new intracellular mRNA imaging probe has been developed that incorporates thiol-terminated hairpin oligonucleotides covalently bound to the surface of citrate-capped gold nanoparticles. The hairpin DNA-coated gold nanoparticles (hAuNPs) positively identifies tyrosinase mRNA in cultured melanoma ce ... [Chem. Commun. 46, 5557 (2010)] published Mon Jul 26, 2010.

Simultaneous electrochemical detection of both PSMA (+) and PSMA (-) prostate cancer cells using an RNA/peptide dual-aptamer probe

Kyoungin Min, Kyung-Mi Song, Minseon Cho, Yang-Sook Chun, Yoon-Bo Shim et al.
Using an RNA/peptide dual-aptamer probe, both PSMA (+) and PSMA (-) prostate cancer cells were simultaneously detected by electrochemical impedance spectroscopy. This approach can be applied as a general tool for early diagnosis of prostate cancer. ... [Chem. Commun. 46, 5566 (2010)] published Mon Jul 26, 2010.

Ultrasensitive and selective DNA detection based on nicking endonuclease assisted signal amplification and its application in cancer cell detection

Sai Bi, Jilei Zhang, and Shusheng Zhang
By significantly circumventing the typical problem of high background induced by excess hemin itself, an ultrasensitive DNA amplified detection method is developed based on nicking endonuclease (NEase) assisted strand scission cycle, which is further successfully applied in cancer cell detection. ... [Chem. Commun. 46, 5509 (2010)] published Mon Jul 26, 2010.

Enhancement of breast CADx with unlabeled data

Andrew R. Jamieson, Maryellen L. Giger, Karen Drukker, and Lorenzo L. Pesce
Purpose: Unlabeled medical image data are abundant, yet the process of converting them into a labeled (truth-known) database is time and resource expensive and fraught with ethical and logistics issues. The authors propose a dual-stage CADx scheme in which both labeled and unlabeled (truth-known and ... [Med. Phys. 37, 4155 (2010)] published Tue Jul 20, 2010.

The diagnostic capability of x-ray scattering parameters for the characterization of breast cancer

Wael M. Elshemey, Omar S. Desouky, Mostafa M. Fekry, Sahar M. Talaat, and Anwar A. Elsayed
Purpose: The evaluation of the diagnostic capability of easy to measure x-ray scattering profile characterization parameters for the detection of breast cancer in excised samples. The selected parameters are the full width at half maximum (FWHM) and area under the x-ray scattering profile of breast ... [Med. Phys. 37, 4257 (2010)] published Thu Jul 22, 2010.

Thermoacoustic molecular tomography with magnetic nanoparticle contrast agents for targeted tumor detection

Liming Nie, Zhongmin Ou, Sihua Yang, and Da Xing
Purpose: The primary feasibility steps of demonstrating the ability of microwave-induced thermoacoustic (TA) in phantoms have been previously reported. However, none were shown to target a diseased site in living subjects in thermoacoustic tomography (TAT) field so far. To determine the expressions ... [Med. Phys. 37, 4193 (2010)] published Wed Jul 21, 2010.

Changes of collagen and nicotinamide adenine dinucleotide in human cancerous and normal prostate tissues studied using native fluorescence spectroscopy with selective excitation wavelength

Yang Pu, Wubao Wang, Guichen Tang, and Robert R. Alfano
The fluorescence spectra of human cancerous and normal prostate tissues obtained by the selective excitation wavelength of 340 nm were measured. The contributions of principle biochemical components to tissue fluorescence spectra were investigated using the method of multivariate curve resolution w ... [J. Biomed. Opt. 15, 047008 ] published .

Evaluating the extent of cell death in 3D high frequency ultrasound by registration with whole-mount tumor histopathology

Roxana M. Vlad, Michael C. Kolios, Joanne L. Moseley, Gregory J. Czarnota, and Kristy K. Brock
Purpose: High frequency ultrasound imaging, 1030 MHz, has the capability to assess tumor response to radiotherapy in mouse tumors as early as 24 h after treatment administration. The advantage of this technique is that the image contrast is generated by changes in the physical properties of dying ce ... [Med. Phys. 37, 4288 (2010)] published Fri Jul 23, 2010.

Label-free discrimination of normal and pulmonary cancer tissues using multiphoton fluorescence ratiometric microscopy

Chun-Chin Wang (王俊欽), Ruei-Jr Wu (吳瑞智), Sung-Jan Lin (林頌然), Yang-Fang Chen (陳永芳), and Chen-Yuan Dong (董成淵)
We performed multiphoton excited autofluorescence and second harmonic generation microscopy for the distinction of normal, lung adenocarcinoma (LAC), and squamous cell carcinoma (SCC) specimens. In addition to morphological distinction, we derived quantitative metrics of cellular redox ratios for ca ... [Appl. Phys. Lett. 97, 043706 (2010)] published Thu Jul 29, 2010.

Scanning elastic scattering spectroscopy detects metastatic breast cancer in sentinel lymph nodes

Martin R. Austwick, Benjamin Clark, Charles A. Mosse, Kristie Johnson, D. Wayne Chicken et al.
A novel method for rapidly detecting metastatic breast cancer within excised sentinel lymph node(s) of the axilla is presented. Elastic scattering spectroscopy (ESS) is a point-contact technique that collects broadband optical spectra sensitive to absorption and scattering within the tissue. A stati ... [J. Biomed. Opt. 15, 047001 (2010)] published Fri Jul 16, 2010.

Photocytotoxicity and DNA cleavage activity of l-arg and l-lys Schiff base oxovanadium(iv) complexes having phenanthroline bases

Pijus K. Sasmal, Ritankar Majumdar, Rajan R. Dighe, and Akhil R. Chakravarty
Oxovanadium(iv) complexes [VO(sal-argH)(B)]Cl () and [VO(sal-lysH)(B)]Cl (), where sal-argH and sal-lysH are N-salicylidene-l-arginine and N-salicylidene-l-lysine Schiff bases and B is a phenanthroline base, viz. 1,10-phenanthroline (phen in and ); dipyrido[3,2-d:2[prime],3[prime]-f]quinoxaline (dp ... [Dalton Trans. 39, 7104 (2010)] published Mon Jul 26, 2010.

Modification of magnetic silica/iron oxide nanocomposites with fluorescent polymethacrylic acid for cancer targeting and drug delivery

Dongyun Chen, Mengjun Jiang, Najun Li, Hongwei Gu, Qingfeng Xu et al.
Biocompatible and water-soluble magnetic nanoparticles with mesoporous core-shell structure were prepared and successfully modified with a fluorescent polymer chain as a labelling segment and folic acid as the cancer targeting moiety and loaded with a drug for directional release. The porous silica ... [J. Mater. Chem. 20, 6422 (2010)] published Wed Jul 28, 2010.

Array comparative genomic hybridization-based characterization of genetic alterations in pulmonary neuroendocrine tumors

Johannes Voortman, Jih-Hsiang Lee, Jonathan Keith Killian, Miia Suuriniemi, Yonghong Wang et al.
The goal of this study was to characterize and classify pulmonary neuroendocrine tumors based on array comparative genomic hybridization (aCGH). Using aCGH, we performed karyotype analysis of 33 small cell lung cancer (SCLC) tumors, 13 SCLC cell lines, 19 bronchial carcinoids, and 9 gastrointestina ... [Proc. Natl. Acad. Sci. U.S.A. 107, 13040 (2010)] published Mon Jul 26, 2010.

Efficacy of bortezomib in a direct xenograft model of primary effusion lymphoma

Kristopher A. Sarosiek, Lucas E. Cavallin, Shruti Bhatt, Ngoc L. Toomey, Yasodha Natkunam et al.
Primary effusion lymphoma (PEL) is an aggressive B-cell lymphoma most commonly diagnosed in HIV-positive patients and universally associated with Kaposi's sarcoma-associated herpesvirus (KSHV). Chemotherapy treatment of PEL yields only short-term remissions in the vast majority of patients, but eff ... [Proc. Natl. Acad. Sci. U.S.A. 107, 13069 (2010)] published Mon Jul 26, 2010.

Long-range function of an intergenic retrotransposon

Wenhu Pi, Xingguo Zhu, Min Wu, Yongchao Wang, Sadanand Fulzele et al.
Retrotransposons including endogenous retroviruses and their solitary long terminal repeats (LTRs) compose >40% of the human genome. Many of them are located in intergenic regions far from genes. Whether these intergenic retrotransposons serve beneficial host functions is not known. Here we show th ... [Proc. Natl. Acad. Sci. U.S.A. 107, 12992 (2010)] published Mon Jul 26, 2010.

RNA-mediated trans-communication can establish paramutation at the b1 locus in maize

Mario Arteaga-Vazquez, Lyudmila Sidorenko, Fernando A. Rabanal, Roli Shrivistava, Kan Nobuta et al.
Paramutation is the epigenetic transfer of information between alleles that leads to the heritable change of expression of one allele. Paramutation at the b1 locus in maize requires seven noncoding tandem repeat (b1TR) sequences located ~100 kb upstream of the transcription start site of b1, and mu ... [Proc. Natl. Acad. Sci. U.S.A. 107, 12986 (2010)] published Mon Jul 26, 2010.

Dnmt3a-Dependent Nonpromoter DNA Methylation Facilitates Transcription of Neurogenic Genes

Hao Wu, Volkan Coskun, Jifang Tao, Wei Xie, Weihong Ge et al.
DNA methylation at proximal promoters facilitates lineage restriction by silencing cell typespecific genes. However, euchromatic DNA methylation frequently occurs in regions outside promoters. The functions of such nonproximal promoter DNA methylation are unclear. Here we show that the de novo DNA m ... [Science 329, 444 (2010)] published Mon Jul 26, 2010.

Mechanisms and implications of transcription blockage by guanine-rich DNA sequences

Boris P. Belotserkovskii, Richard Liu, Silvia Tornaletti, Maria M. Krasilnikova, Sergei M. Mirkin et al.
Various DNA sequences that interfere with transcription due to their unusual structural properties have been implicated in the regulation of gene expression and with genomic instability. An important example is sequences containing G-rich homopurine-homopyrimidine stretches, for which unusual trans ... [Proc. Natl. Acad. Sci. U.S.A. 107, 12816 (2010)] published Mon Jul 26, 2010.

Surprising gene expression patterns within and between PDF-containing circadian neurons in Drosophila

Elzbieta Kula-Eversole, Emi Nagoshi, Yuhua Shang, Joseph Rodriguez, Ravi Allada et al.
To compare circadian gene expression within highly discrete neuronal populations, we separately purified and characterized two adjacent but distinct groups of Drosophila adult circadian neurons: the 8 small and 10 large PDF-expressing ventral lateral neurons (s-LNvs and l-LNvs, respectively). The s ... [Proc. Natl. Acad. Sci. U.S.A. 107, 13497 (2010)] published Wed Jul 28, 2010.

A Nitrospira metagenome illuminates the physiology and evolution of globally important nitrite-oxidizing bacteria

Sebastian Lucker, Michael Wagner, Frank Maixner, Eric Pelletier, Hanna Koch et al.
Nitrospira are barely studied and mostly uncultured nitrite-oxidizing bacteria, which are, according to molecular data, among the most diverse and widespread nitrifiers in natural ecosystems and biological wastewater treatment. Here, environmental genomics was used to reconstruct the complete genom ... [Proc. Natl. Acad. Sci. U.S.A. 107, 13479 (2010)] published Wed Jul 28, 2010.

A time-invariant principle of genome evolution

Subhajyoti De and M. Madan Babu
Uncovering general principles of genome evolution that are time-invariant and that operate in germ and somatic cells has implications for genome-wide association studies (GWAS), gene therapy, and disease genomics. Here we investigate the relationship between structural alterations (e.g., insertions ... [Proc. Natl. Acad. Sci. U.S.A. 107, 13004 (2010)] published Mon Jul 26, 2010.

Global analysis of trans-splicing in Drosophila

C. Joel McManus, Michael O. Duff, Jodi Eipper-Mains, and Brenton R. Graveley
Precursor mRNA (pre-mRNA) splicing can join exons contained on either a single pre-mRNA (cis) or on separate pre-mRNAs (trans). It is exceedingly rare to have trans-splicing between protein-coding exons and has been demonstrated for only two Drosophila genes: mod(mdg4) and lola. It has also been su ... [Proc. Natl. Acad. Sci. U.S.A. 107, 12975 (2010)] published Mon Jul 26, 2010.

Cross-species genomics matches driver mutations and cell compartments to model ependymoma

Robert A. Johnson, Karen D. Wright, Helen Poppleton, Kumarasamypet M. Mohankumar, David Finkelstein et al.
Understanding the biology that underlies histologically similar but molecularly distinct subgroups of cancer has proven difficult because their defining genetic alterations are often numerous, and the cellular origins of most cancers remain unknown. We sought to decipher this heterogeneity by integ ... [Nature 466, 632 (2010)] published Thu Jul 29, 2010.

Genetic flexibility of regulatory networks

Alexander Hunziker, Csaba Tuboly, Peter Horvath, Sandeep Krishna, and Szabolcs Semsey
Gene regulatory networks are based on simple building blocks such as promoters, transcription factors (TFs) and their binding sites on DNA. But how diverse are the functions that can be obtained by different arrangements of promoters and TF binding sites? In this work we constructed synthetic regul ... [Proc. Natl. Acad. Sci. U.S.A. 107, 12998 (2010)] published Mon Jul 26, 2010.

Network motifs come in sets: Correlations in the randomization process

Reid Ginoza and Andrew Mugler
The identification of motifssubgraphs that appear significantly more often in a particular network than in an ensemble of randomized networkshas become a ubiquitous method for uncovering potentially important subunits within networks drawn from a wide variety of fields. We find that the most common ... [Phys. Rev. E 82, 011921 ] published .

Biological role of noise encoded in a genetic network motif

Mark Kittisopikul and Gurol M. Suel
Genetic circuits that regulate distinct cellular processes can differ in their wiring pattern of interactions (architecture) and susceptibility to stochastic fluctuations (noise). Whether the link between circuit architecture and noise is of biological importance remains, however, poorly understood ... [Proc. Natl. Acad. Sci. U.S.A. 107, 13300 (2010)] published Wed Jul 28, 2010.

Motif distributions in phase-space networks for characterizing experimental two-phase flow patterns with chaotic features

Zhong-Ke Gao, Ning-De Jin, Wen-Xu Wang, and Ying-Cheng Lai
The dynamics of two-phase flows have been a challenging problem in nonlinear dynamics and fluid mechanics. We propose a method to characterize and distinguish patterns from inclined water-oil flow experiments based on the concept of network motifs that have found great usage in network science and s ... [Phys. Rev. E 82, 016210 ] published .

Calcium window currents, periodic forcing, and chaos: Understanding single neuron response with a discontinuous one-dimensional map

J. Laudanski, C. Sumner, and S. Coombes
Thalamocortical (TC) neurones are known to express the low-voltage activated, inactivating Ca current I. The triggering of this current underlies the generation of low threshold Ca potentials that may evoke single or bursts of action potentials. Moreover, this current can contribute to an intrinsic ... [Phys. Rev. E 82, 011924 ] published .

Integrative Modeling Defines the Nova Splicing-Regulatory Network and Its Combinatorial Controls

Chaolin Zhang, Maria A. Frias, Aldo Mele, Matteo Ruggiu, Taesun Eom et al.
The control of RNA alternative splicing is critical for generating biological diversity. Despite emerging genome-wide technologies to study RNA complexity, reliable and comprehensive RNA-regulatory networks have not been defined. Here, we used Bayesian networks to probabilistically model diverse dat ... [Science 329, 439 (2010)] published Mon Jul 26, 2010.

Josephson junction simulation of neurons

Patrick Crotty, Dan Schult, and Ken Segall
With the goal of understanding the intricate behavior and dynamics of collections of neurons, we present superconducting circuits containing Josephson junctions that model biologically realistic neurons. These Josephson junction neurons reproduce many characteristic behaviors of biological neurons s ... [Phys. Rev. E 82, 011914 ] published .

Sparse coding and high-order correlations in fine-scale cortical networks

Ifije E. Ohiorhenuan, Ferenc Mechler, Keith P. Purpura, Anita M. Schmid, Qin Hu et al.
Connectivity in the cortex is organized at multiple scales, suggesting that scale-dependent correlated activity is particularly important for understanding the behaviour of sensory cortices and their function in stimulus encoding. We analysed the scale-dependent structure of cortical interactions b ... [Nature 466, 617 (2010)] published Thu Jul 29, 2010.

Problems of coding stereo images in human memory

G. Krumina and V. A. Lyakhovetskii
This paper discusses the memorization and recall by man of a sequence of planar or stereoscopic images, including six frames that contain a planar strip (8 x 8 positions of the stimulus) or a volume strip (8 x 4 x 2 positions). At the recall stage, the subject chose between the stimulus and three di ... [J. Opt. Technol. 77, 417 (2010)] published Wed Jul 28, 2010.

Partitioning networks into clusters and residuals with average association

Martin Vejmelka and Milan Palus
We investigate the problem of detecting clusters exhibiting higher-than-average internal connectivity in networks of interacting systems. We show how the average association objective formulated in the context of spectral graph clustering leads naturally to a clustering strategy where each system is ... [Chaos 20, 033103 (2010)] published Fri Jul 23, 2010.

Astrocytes Control Breathing Through pH-Dependent Release of ATP

Alexander V. Gourine, Vitaliy Kasymov, Nephtali Marina, Feige Tang, Melina F. Figueiredo et al.
Astrocytes provide structural and metabolic support for neuronal networks, but direct evidence demonstrating their active role in complex behaviors is limited. Central respiratory chemosensitivity is an essential mechanism that, via regulation of breathing, maintains constant levels of blood and bra ... [Science 329, 571 ] published .

Stability of graph communities across time scales

J.-C. Delvenne, S. N. Yaliraki, and M. Barahona
The complexity of biological, social, and engineering networks makes it desirable to find natural partitions into clusters (or communities) that can provide insight into the structure of the overall system and even act as simplified functional descriptions. Although methods for community detection ... [Proc. Natl. Acad. Sci. U.S.A. 107, 12755 (2010)] published Mon Jul 26, 2010.

Fourier analysis and systems identification of the p53 feedback loop

Naama Geva-Zatorsky, Erez Dekel, Eric Batchelor, Galit Lahav, and Uri Alon
A key circuit in the response of cells to damage is the p53mdm2 feedback loop. This circuit shows sustained, noisy oscillations in individual human cells following DNA breaks. Here, we apply an engineering approach known as systems identification to quantify the in vivo interactions in the circuit ... [Proc. Natl. Acad. Sci. U.S.A. 107, 13550 (2010)] published Wed Jul 28, 2010.

Modeling light propagation through bacterial colonies and its correlation with forward scattering patterns

Euiwon Bae, Nan Bai, Amornrat Aroonnual, J. Paul Robinson, Arun K. Bhunia et al.
Bacterial colonies play an important role in the isolation and identification of bacterial species, and plating on a petri dish is still regarded as the gold standard for confirming the cause of an outbreak situation. A bacterial colony consists of millions of densely packed individual bacteria alo ... [J. Biomed. Opt. 15, 045001 (2010)] published Fri Jul 16, 2010.

Fixed points and limit cycles in the population dynamics of lysogenic viruses and their hosts

Zhenyu Wang and Nigel Goldenfeld
Starting with stochastic rate equations for the fundamental interactions between microbes and their viruses, we derive a mean-field theory for the population dynamics of microbe-virus systems, including the effects of lysogeny. In the absence of lysogeny, our model is a generalization of that propos ... [Phys. Rev. E 82, 011918 ] published .

3D visualization of HIV transfer at the virological synapse between dendritic cells and T cells

Richard L. Felts, Kedar Narayan, Jacob D. Estes, Dan Shi, Charles M. Trubey et al.
The efficiency of HIV infection is greatly enhanced when the virus is delivered at conjugates between CD4 T cells and virus-bearing antigen-presenting cells such as macrophages or dendritic cells via specialized structures known as virological synapses. Using ion abrasion SEM, electron tomography, ... [Proc. Natl. Acad. Sci. U.S.A. 107, 13336 (2010)] published Wed Jul 28, 2010.

Btbd7 Regulates Epithelial Cell Dynamics and Branching Morphogenesis

Tomohiro Onodera, Takayoshi Sakai, Jeff Chi-feng Hsu, Kazue Matsumoto, John A. Chiorini et al.
During embryonic development, many organs form by extensive branching of epithelia through the formation of clefts and buds. In cleft formation, buds are delineated by the conversion of epithelial cell-cell adhesions to cell-matrix adhesions, but the mechanisms of cleft formation are not clear. We h ... [Science 329, 562 ] published .

Directed assembly of yeast cells into living yeastosomes by microbubble templating

Marie-Laure Brandy, Olivier J. Cayre, Rawil F. Fakhrullin, Orlin D. Velev, and Vesselin N. Paunov
We report the fabrication of yeastosomesnovel multicellular assemblies, which consist of a spherical monolayer of living yeast cells held together by colloid interactions. Our method is based on templating of microbubbles with cells coated with cationic polyelectrolyte and the layer-by-layer techniq ... [Soft Matter 6, 3494 ] published .

Beyond the Death of Linear Response: 1/f Optimal Information Transport

Gerardo Aquino, Mauro Bologna, Paolo Grigolini, and Bruce J. West
Nonergodic renewal processes have recently been shown by several authors to be insensitive to periodic perturbations, thereby apparently sanctioning the death of linear response, a building block of nonequilibrium statistical physics. We show that it is possible to go beyond the death of linear resp ... [Phys. Rev. Lett. 105, 040601 ] published .

Information-Optimal Transcriptional Response to Oscillatory Driving

Andrew Mugler, Aleksandra M. Walczak, and Chris H. Wiggins
Intracellular transmission of information via chemical and transcriptional networks is thwarted by a physical limitation: The finite copy number of the constituent chemical species introduces unavoidable intrinsic noise. Here we solve for the complete probabilistic description of the intrinsically n ... [Phys. Rev. Lett. 105, 058101 ] published .

Correct biological timing in Arabidopsis requires multiple light-signaling pathways

Neil Dalchau, Katharine E. Hubbard, Fiona C. Robertson, Carlos T. Hotta, Helen M. Briggs et al.
Circadian oscillators provide rhythmic temporal cues for a range of biological processes in plants and animals, enabling anticipation of the day/night cycle and enhancing fitness-associated traits. We have used engineering models to understand the control principles of a plant's response to seasona ... [Proc. Natl. Acad. Sci. U.S.A. 107, 13171 (2010)] published Mon Jul 26, 2010.

Erratum: Memristive model of amoeba learning [Phys. Rev. E 80, 021926 (2009)]

Yuriy V. Pershin, Steven La Fontaine, and Massimiliano Di Ventra
Abstract not available. [Phys. Rev. E 82, 019904 ] published .

An improved Bayesian tensor regularization and sampling algorithm to track neuronal fiber pathways in the language circuit

Arabinda Mishra, Adam W. Anderson, Xi Wu, John C. Gore, and Zhaohua Ding
Purpose: The purpose of this work is to design a neuronal fiber tracking algorithm, which will be more suitable for reconstruction of fibers associated with functionally important regions in the human brain. The functional activations in the brain normally occur in the gray matter regions. Hence the ... [Med. Phys. 37, 4274 (2010)] published Thu Jul 22, 2010.

Physical Limits on Cellular Sensing of Spatial Gradients

Bo Hu, Wen Chen, Wouter-Jan Rappel, and Herbert Levine
Many eukaryotic cells are able to detect chemical gradients by directly measuring spatial concentration differences. The precision of such gradient sensing is limited by fluctuations in the binding of diffusing particles to specific receptors on the cell surface. Here, we explore the physical limits ... [Phys. Rev. Lett. 105, 048104 ] published .

Local Cochlear Correlations of Perceived Pitch

Stefan Martignoli and Ruedi Stoop
Pitch is one of the most salient attributes of the human perception of sound, but is still not well understood. This difficulty originates in the entwined nature of the phenomenon, in which a physical stimulus as well as a psychophysiological signal receiver are involved. In an electronic realizatio ... [Phys. Rev. Lett. 105, 048101 ] published .

How wing compliance drives the efficiency of self-propelled flapping flyers

Benjamin Thiria and Ramiro Godoy-Diana
Wing flexibility governs the flying performance of flapping-wing flyers. Here, we use a self-propelled flapping-wing model mounted on a merry go round to investigate the effect of wing compliance on the propulsive efficiency of the system. Our measurements show that the elastic nature of the wings c ... [Phys. Rev. E 82, 015303 ] published .

Mosquito proboscis: An elegant biomicroelectromechanical system

X. Q. Kong and C. W. Wu
The mouthparts of female mosquitoes have evolved to form a special proboscis, a natural biomicroelectromechanical system (BMEMS), which is used for painlessly penetrating human skin and sucking blood. Scanning electron microscope observations show that the mosquito proboscis consists of a small bund ... [Phys. Rev. E 82, 011910 ] published .

Image correlation spectroscopy as a tool for microrheology of soft materials

Nicholas Agung Kurniawan, Chwee Teck Lim, and Raj Rajagopalan
Image correlation spectroscopy (ICS) has been mostly used to quantify spatiotemporal events in biological experiments. Here, we develop and demonstrate the use of ICS for microrheology ([mu]R) of complex, viscoelastic materials. A special technique for extracting mean-squared displacements (MSD) of ... [Soft Matter 6, 3499 ] published .

Measurement of Elastic Properties of Tissue by Shear Wave Propagation Generated by Acoustic Radiation Force

Marie Tabaru, Takashi Azuma, and Kunio Hashiba
Acoustic radiation force (ARF) imaging has been developed as a novel elastography technology to diagnose hepatic disease and breast cancer. The accuracy of shear wave speed estimation, which is one of the applications of ARF elastography, is studied. The Young's moduli of pig liver and foie gras ... [Jpn. J. Appl. Phys. 49, 07HF09 (2010)] published Mon Jul 26, 2010.

Regulation of cell motile behavior by crosstalk between cadherin- and integrin-mediated adhesions

Nicolas Borghi, Molly Lowndes, Venkat Maruthamuthu, Margaret L. Gardel, and W. James Nelson
During normal development and in disease, cohesive tissues undergo rearrangements that require integration of signals from cell adhesions to neighboring cells and to the extracellular matrix (ECM). How a range of cell behaviors is coordinated by these different adhesion complexes is unknown. To ana ... [Proc. Natl. Acad. Sci. U.S.A. 107, 13324 (2010)] published Wed Jul 28, 2010.

Functional Modules and Structural Basis of Conformational Coupling in Mitochondrial Complex I

Carola Hunte, Volker Zickermann, and Ulrich Brandt
Proton-pumping respiratory complex I is one of the largest and most complicated membrane protein complexes. Its function is critical for efficient energy supply in aerobic cells, and malfunctions are implicated in many neurodegenerative disorders. Here, we report an x-ray crystallographic analysis o ... [Science 329, 448 (2010)] published Mon Jul 26, 2010.

Biophotonic probing of macromolecular transformations during apoptosis

Artem Pliss, Andrey N. Kuzmin, Aliaksandr V. Kachynski, and Paras N. Prasad
We introduce here multiplex nonlinear optical imaging as a powerful tool for studying the molecular organization and its transformation in cellular processes, with the specific example of apoptosis. Apoptosis is a process of self-initiated cell death, critically important for physiological regulati ... [Proc. Natl. Acad. Sci. U.S.A. 107, 12771 (2010)] published Mon Jul 26, 2010.

Substrate-mediated crosstalk between elastic pillars

Ingmar Schoen
Cellular traction forces are routinely measured on arrays of flexible microscopic pillars whose deflections are regarded as independent. Here it is shown that vertical deformations of the underlying elastic substrate constitute a coupling between individual pillars. The crosstalk is dominated by a f ... [Appl. Phys. Lett. 97, 023703 (2010)] published Fri Jul 16, 2010.

Self-assembled autonomous runners and tumblers

Stephen Ebbens, Richard A. L. Jones, Anthony J. Ryan, Ramin Golestanian, and Jonathan R. Howse
A class of artificial microswimmers with combined translational and rotational self-propulsion is studied experimentally. The chemically fueled microswimmers are made of doublets of Janus colloidal beads with catalytic patches that are positioned at a fixed angle relative to one another. The mean-sq ... [Phys. Rev. E 82, 015304 ] published .

Molecular origin of strain softening in cross-linked F-actin networks

Hyungsuk Lee, Jorge M. Ferrer, Matthew J. Lang, and Roger D. Kamm
Two types of measurement are presented that relate molecular events to macroscopic behavior of F-actin networks. First, shear modulus is measured by oscillating an embedded microbead. Second, a microbead is translated at constant rate and transitions in the resisting force are observed. The loading ... [Phys. Rev. E 82, 011919 ] published .

Mesoporous bioactive glass coatings on stainless steel for enhanced cell activity, cytoskeletal organization and AsMg immobilization

Xiupeng Wang, Xia Li, Kazuo Onuma, Atsuo Ito, Yu Sogo et al.
Mesoporous bioactive glass (MBG) coatings with SiO : CaO : PO mol ratio of 100 : 0 : 0, 80 : 15 : 5 and 70 : 25 : 5 and a tunable pore size and pore structure were prepared on a stainless steel plate by spin-coating sol solutions containing a triblock copolymer and the inorganic precursors. The calc ... [J. Mater. Chem. 20, 6437 (2010)] published Wed Jul 28, 2010.

Microtubule-assisted mechanism for functional metabolic macromolecular complex formation

Songon An, Yijun Deng, John W. Tomsho, Minjoung Kyoung, and Stephen J. Benkovic
Evidence has been presented for a metabolic multienzyme complex, the purinosome, that participates in de novo purine biosynthesis to form clusters in the cytoplasm of living cells under purine-depleted conditions. Here we identified, using fluorescent live cell imaging, that a microtubule network a ... [Proc. Natl. Acad. Sci. U.S.A. 107, 12872 (2010)] published Mon Jul 26, 2010.

Kinetics of Myosin Node Aggregation into a Contractile Ring

Nikola Ojkic and Dimitrios Vavylonis
We study a stochastic aggregation model for the assembly of the contractile ring from a broad band of nodes during cytokinesis in fission yeast. We found that bands of nodes condense into rings when the range of node interactions is larger than the width of the band. Wide bands are unstable to clump ... [Phys. Rev. Lett. 105, 048102 ] published .

Topological Defects in Twisted Bundles of Two-Dimensionally Ordered Filaments

Gregory M. Grason
Twisted assemblies of filaments in ropes, cables, and bundles are essential structural elements in both macroscopic materials and living organisms. We develop the unique, nonlinear elastic properties of twisted filament bundles that derive from generic properties of two-dimensional line-ordered mate ... [Phys. Rev. Lett. 105, 045502 ] published .

Combined multiphoton imaging and automated functional enucleation of porcine oocytes using femtosecond laser pulses

Kai Kuetemeyer, Andrea Lucas-Hahn, Bjoern Petersen, Erika Lemme, Petra Hassel et al.
Since the birth of Dolly as the first mammal cloned from a differentiated cell, somatic cell cloning has been successful in several mammalian species, albeit at low success rates. The highly invasive mechanical enucleation step of a cloning protocol requires sophisticated, expensive equipment and co ... [J. Biomed. Opt. 15, 046006 (2010)] published Wed Jul 21, 2010.

Neuron adhesion and strengthening

Aracely Rocha, Kuihuan Jian, Gladys Ko, and Hong Liang
Understanding the neuron/material adhesion is important for neuron stimulation and growth. The current challenges remain in the lack of precision of measuring techniques and understanding the behavior of neuron. Here, we report a fluid shear method to investigate adhesion at the neuron/poly-D-lysine ... [J. Appl. Phys. 108, 024702 (2010)] published Mon Jul 26, 2010.

Dynamics of the tug-of-war model for cellular transport

Yunxin Zhang and Michael E. Fisher
The transport of organelles and other cargoes in living cells has been described by a kinetic tug-of-war model advanced by Muller, Klumpp, and Lipowsky, in which, as a function of time, t, a team of n(t)=0,1,[centered ellipsis],N molecular motors may attach a cargo to a filamentous track and pull it ... [Phys. Rev. E 82, 011923 ] published .

Cavitation rheology of the vitreous: mechanical properties of biological tissue

Jessica A. Zimberlin, Jennifer J. McManus, and Alfred J. Crosby
We demonstrate the importance of measuring the mechanical properties of biological tissue in vivo by quantifying the mechanical properties of bovine vitreous both in its native state and upon removal from the eye. The mechanical properties are determined by the cavitation rheology technique develope ... [Soft Matter 6, 3632 ] published .

Codon thermoelectric signature in molecular junctions

Enrique Macia
The thermoelectric power of trimer oligonucleotides connected in between metallic contacts at different temperatures is theoretically studied. The obtained analytical expressions reveal the existence of important resonance effects leading to a significant thermopower enhancement for certain characte ... [Phys. Rev. B 82, 045431 ] published .

Publisher's Note: Two-component magnetic structure of iron oxide nanoparticles mineralized in Listeria innocua protein cages [J. Appl. Phys. 107, 114703 (2010)]

Robert J. Usselman, Michael T. Klem, Stephen E. Russek, Mark Young, Trevor Douglas et al.
Abstract not available. [J. Appl. Phys. 108, 029903 (2010)] published Fri Jul 30, 2010.

Evidence of preferential pi-stacking: a study of intermolecular and intramolecular charge transfer complexes

N. S. Saleesh Kumar, Maneesh D. Gujrati, and James N. Wilson
Nine combinations of pi-electron donors and acceptors were examined by UV-vis, fluorescence and H-NMR spectroscopy to identify pi-stacked charge transfer complexes in macromolecular and supramolecular constructs. The high association constant of pyrene and naphthalene diimide suggests a preferential ... [Chem. Commun. 46, 5464 (2010)] published Mon Jul 26, 2010.

Pseudoracemic amino acid complexes: blind predictions for flexible two-component crystals

Carl Henrik Gorbitz, Bjorn Dalhus, and Graeme M. Day
Ab initio prediction of the crystal packing in complexes between two flexible molecules is a particularly challenging computational chemistry problem. In this work we present results of single crystal structure determinations as well as theoretical predictions for three 1 : 1 complexes between hydro ... [Phys. Chem. Chem. Phys. 12, 8466 (2010)] published Mon Jul 26, 2010.

Strong reversible Fe-mediated bridging between dopa-containing protein films in water

Hongbo Zeng, Dong Soo Hwang, Jacob N. Israelachvili, and J. Herbert Waite
Metal-containing polymer networks are widespread in biology, particularly for load-bearing exoskeletal biomaterials. Mytilus byssal cuticle is an especially interesting case containing moderate levels of Fe and cuticle proteinmussel foot protein-1 (mfp-1), which has a peculiar combination of high h ... [Proc. Natl. Acad. Sci. U.S.A. 107, 12850 (2010)] published Mon Jul 26, 2010.

Amino/guanidino-functionalized N-(pyrrolidin-2-ethyl)glycine-based pet-PNA: Design, synthesis and binding with DNA/RNA

Sachin S. Gokhale and Vaijayanti A. Kumar
The N-(pyrrolidin-2-ethyl) glycine-based PNA (pet-PNA) backbone, with 4-amino or 4-guanidino-functionalized pyrrolidine ring, confers constrained conformational flexibility on aegPNA. The oligomers bind to the target DNA and RNA sequences with increased sequence specificity and antiparallel versus p ... [Org. Biomol. Chem. 8, 3742 (2010)] published Thu Jul 29, 2010.

Subnanometre single-molecule localization, registration and distance measurements

Alexandros Pertsinidis, Yunxiang Zhang, and Steven Chu
Remarkable progress in optical microscopy has been made in the measurement of nanometre distances. If diffraction blurs the image of a point object into an Airy disk with a root-mean-squared (r.m.s.) size of s = 0.44/2NA (90nm for light with a wavelength of = 600nm and an objective lens with a num ... [Nature 466, 647 (2010)] published Thu Jul 29, 2010.

Quantifying E. coli Proteome and Transcriptome with Single-Molecule Sensitivity in Single Cells

Yuichi Taniguchi, Paul J. Choi, Gene-Wei Li, Huiyi Chen, Mohan Babu et al.
Protein and messenger RNA (mRNA) copy numbers vary from cell to cell in isogenic bacterial populations. However, these molecules often exist in low copy numbers and are difficult to detect in single cells. We carried out quantitative system-wide analyses of protein and mRNA expression in individual ... [Science 329, 533 ] published .

Detecting origins of subdiffusion: P-variation test for confined systems

Marcin Magdziarz and Joseph Klafter
In this paper, we propose a method to distinguish between mechanisms leading to single molecule subdiffusion in confinement. We show that the method of p-variation, introduced in the recent paper [M. Magdziarz et al., Phys. Rev. Lett. 103, 180602 (2009)], can be successfully applied also for confine ... [Phys. Rev. E 82, 011129 ] published .

Stochastic heating of a molecular nanomagnet

L. Chotorlishvili, P. Schwab, Z. Toklikishvili, and J. Berakdar
We study the excitation dynamics of a single molecular nanomagnet by static and pulsed magnetic fields. Based on a stability analysis of the classical magnetization dynamics we identify analytically the fields parameters for which the energy is stochastically pumped into the system in which case the ... [Phys. Rev. B 82, 014418 ] published .

Discrimination of N6-methyl adenine in a specific DNA sequence

Chikara Dohno, Tomonori Shibata, and Kazuhiko Nakatani
We have developed a novel chemistry-based method to detect adenine methylation. A DNA probe functionalized with a formyl group discriminates between adenine and N6-methyl adenine by the formation of a selective interstrand cross-link. ... [Chem. Commun. 46, 5530 (2010)] published Mon Jul 26, 2010.

Single-molecule denaturation mapping of DNA in nanofluidic channels

Walter Reisner, Niels B. Larsen, Asli Silahtaroglu, Anders Kristensen, Niels Tommerup et al.
Here we explore the potential power of denaturation mapping as a single-molecule technique. By partially denaturing YOYO[registered sign]-1-labeled DNA in nanofluidic channels with a combination of formamide and local heating, we obtain a sequence-dependent "barcode" corresponding to a series of lo ... [Proc. Natl. Acad. Sci. U.S.A. 107, 13294 (2010)] published Wed Jul 28, 2010.

Fluorescence enhancement of single DNA molecules confined in Si/SiO nanochannels

Fredrik Westerlund, Fredrik Persson, Anders Kristensen, and Jonas O. Tegenfeldt
We demonstrate that the detected emission intensity from YOYO-labeled DNA molecules confined in 180 nm deep Si/SiO nanofunnels changes significantly and not monotonically with the width of the funnel. This effect may be of importance for quantitative fluorescence microscopy and for experiments with ... [Lab Chip 10, 2049 (2010)] published Wed Jul 28, 2010.

Persistence length of DNA molecules confined in nanochannels

Peter Cifra, Zuzana Benkova, and Tomas Bleha
The influence of confinement on the persistence length of dsDNA molecules under a high ionic strength environment was explored by coarse-grained Monte Carlo simulations in channels of different profiles. It was found that under confinement three definitions of the persistence length of DNA molecules ... [Phys. Chem. Chem. Phys. 12, 8934 (2010)] published Thu Jul 29, 2010.

Structural stability versus conformational sampling in biomolecular systems: Why is the charge transfer efficiency in G4-DNA better than in double-stranded DNA?

P. Benjamin Woiczikowski, Tomas Kubar, Rafael Gutierrez, Gianaurelio Cuniberti, and Marcus Elstner
The electrical conduction properties of G4-DNA are investigated using a hybrid approach, which combines electronic structure calculations, molecular dynamics (MD) simulations, and the formulation of an effective tight-binding model Hamiltonian. Charge transport is studied by computing transmission f ... [J. Chem. Phys. 133, 035103 (2010)] published Mon Jul 19, 2010.

An injectable paste of calcium phosphate nanorods, functionalized with nucleic acids, for cell transfection and gene silencing

J. Klesing, S. Chernousova, A. Kovtun, S. Neumann, L. Ruiz et al.
Calcium phosphate nanorods which are typically used as paste for bone substitution were functionalized by DNA or siRNA. The structure and morphology of the nanorods did not change by the functionalization as indicated by dynamic light scattering (DLS), scanning electron microscopy (SEM), and high-re ... [J. Mater. Chem. 20, 6144 (2010)] published Mon Jul 26, 2010.

Theoretical Description of a DNA-Linked Nanoparticle Self-Assembly

Chia Wei Hsu, Francesco Sciortino, and Francis W. Starr
Nanoparticles tethered with DNA strands are promising building blocks for bottom-up nanotechnology, and a theoretical understanding is important for future development. Here we build on approaches developed in polymer physics to provide theoretical descriptions for the equilibrium clustering and dyn ... [Phys. Rev. Lett. 105, 055502 ] published .

DNA separation on surfaces

Avital Braiman, Thomas Thundat, and Fedor Rudakov
Recent experimental work on DNA separation on surfaces reveals a power law behavior of the mobility with size. We employed a simple model that elucidates the observed power law trend. When the external electric field is barely larger than the critical value required for initiating translational moti ... [Appl. Phys. Lett. 97, 033703 ] published .

DNA translocation through an array of kinkednanopores

Zhu Chen, Yingbing Jiang, Darren R. Dunphy, David P. Adams, Carter Hodges et al.
Synthetic solid-state nanopores are being intensively investigated as single-molecule sensors for detection and characterization of DNA, RNA and proteins. This field has been inspired by the exquisite selectivity and flux demonstrated by natural biological channels and the dream of emulating these b ... [Nature Mater. 9, 667 (2010)] published Mon Jul 26, 2010.

Cytochrome c polymerization by successive domain swapping at the C-terminal helix

Shun Hirota, Yoko Hattori, Satoshi Nagao, Midori Taketa, Hirofumi Komori et al.
Cytochrome c (cyt c) is a stable protein that functions in a monomeric state as an electron donor for cytochrome c oxidase. It is also released to the cytosol when permeabilization of the mitochondrial outer membrane occurs at the early stage of apoptosis. For nearly half a century, it has been kno ... [Proc. Natl. Acad. Sci. U.S.A. 107, 12854 (2010)] published Mon Jul 26, 2010.

Inverting the enantioselectivity of P450pyr monooxygenase by directed evolution

Weng Lin Tang, Zhi Li, and Huimin Zhao
We report the first example of directed evolution of a P450 monooxygenase with inverted enantioselectivity for asymmetric biohydroxylation. The biohydroxylation product of the best mutant 1AF4A has an ee of 83% (R) compared to the wild type's ee of 43% (S). ... [Chem. Commun. 46, 5461 (2010)] published Mon Jul 26, 2010.

Analysis of binding behavior between dynamic structures of a papain and the peptide consisting of 10 GLY residues

Katsuhiko Nishiyama
The binding of 10GLY to dynamic structures of papain was investigated by molecular dynamics and docking simulations. The binding free energies and sites were greatly fluctuated depending on the time and the binding was more stable and existed at the near site of active center when the structural cha ... [J. Appl. Phys. 108, 024701 (2010)] published Thu Jul 22, 2010.

Ab initio analysis of the x-ray absorption spectrum of the myoglobincarbon monoxide complex: Structure and vibrations

G. Veronesi, C. Degli Esposti Boschi, L. Ferrari, G. Venturoli, F. Boscherini et al.
We present a comparison between Fe K-edge x-ray absorption spectra of carbonmonoxymyoglobin and its simulation based on density-functional theory determination of the structure and vibrations and spectral simulation with multiple-scattering theory. An excellent comparison is obtained for the main pa ... [Phys. Rev. B 82, 020101 ] published .

Cooperativity at different space and time scales in multiscale protein dynamics

Yasuhiro Matsunaga, Chun-Biu Li, and Tamiki Komatsuzaki
A method proposed by Matsunaga et al. [Phys. Rev. Lett. 99, 238103 (2007)] is applied to simple stochastic models and two model proteins composed of 46 amino beads with three different kinds of residues. The method, which is based on the combination of the principal component analysis and the finite ... [Phys. Rev. E 82, 016213 ] published .

Entropic potential field formed for a linear-motor protein near a filament: Statistical-mechanical analyses using simple models

Ken-ichi Amano, Takashi Yoshidome, Mitsuhiro Iwaki, Makoto Suzuki, and Masahiro Kinoshita
We report a new progress in elucidating the mechanism of the unidirectional movement of a linear-motor protein (e.g., myosin) along a filament (e.g., F-actin). The basic concept emphasized here is that a potential field is entropically formed for the protein on the filament immersed in solvent due t ... [J. Chem. Phys. 133, 045103 (2010)] published Tue Jul 27, 2010.

Infrared signatures of the peptide dynamical transition: A molecular dynamics simulation study

Maja Kobus, Phuong H. Nguyen, and Gerhard Stock
Recent two-dimensional infrared (2D-IR) experiments on a short peptide 3-helix in chloroform solvent [E. H. G. Backus et al., J. Phys. Chem. B 113, 13405 (2009)] revealed an intriguing temperature dependence of the homogeneous line width, which was interpreted in terms of a dynamical transition of t ... [J. Chem. Phys. 133, 034512 (2010)] published Tue Jul 20, 2010.

Excited state geometry of photoactive yellow protein chromophore: A combined conductorlike polarizable continuum model and time-dependent density functional study

Yali Wang and Hui Li
Analytic gradient of the combined conductorlike polarizable continuum model (CPCM) and time-dependent density functional theory method is derived and implemented. Due to the use of the fixed points with variable areas tessellation scheme, the excited state potential energy surfaces (PESs) are rigoro ... [J. Chem. Phys. 133, 034108 (2010)] published Mon Jul 19, 2010.

Topological solitons and folded proteins

Maxim Chernodub, Shuangwei Hu, and Antti J. Niemi
We argue that protein loops can be described by topological domain-wall solitons that interpolate between ground states which are the alpha helices and beta strands. We present an energy function that realizes loops as soliton solutions to its equation of motion, and apply these solitons to model a ... [Phys. Rev. E 82, 011916 ] published .

Normal modes and phase transition of the protein chain based on the Hamiltonian formalism

Hon-Wai Leong, Lock Yue Chew, and Kerson Huang
We use the torsional angles of the protein chain as generalized coordinates in the canonical formalism, derive canonical equations of motion, and investigate the coordinate dependence of the kinetic energy expressed in terms of the canonical momenta. We use the formalism to compute the normal-freque ... [Phys. Rev. E 82, 011915 ] published .

Dominant reaction pathways in protein folding: A direct validation against molecular dynamics simulations

Pietro Faccioli, Alice Lonardi, and Henri Orland
The dominant reaction pathway (DRP) is an algorithm to microscopically compute the most probable reaction pathways in the overdamped Langevin dynamics without investing computational time in simulating the local thermal motion in the metastable configurations. In order to test the accuracy of such a ... [J. Chem. Phys. 133, 045104 (2010)] published Thu Jul 29, 2010.

Cooperative formation of native-like tertiary contacts in the ensemble of unfolded states of a four-helix protein

Susanne W. Bruun, Vytautas IesmantaviCius, Jens Danielsson, and Flemming M. Poulsen
In studies of the ensembles of unfolded structures of a four-helix bundle protein, we have detected the presence of potential precursors of native tertiary structures. These observations were based on the perturbation of NMR chemical shifts of the protein backbone atoms by single site mutations. So ... [Proc. Natl. Acad. Sci. U.S.A. 107, 13306 (2010)] published Wed Jul 28, 2010.

Properties of knotted ring polymers. II. Transport properties

Marc L. Mansfield and Jack F. Douglas
We have calculated the hydrodynamic radius R and intrinsic viscosity [eta] of both lattice self-avoiding rings and lattice theta-state rings that are confined to specific knot states by our path-integration technique. We observe that naive scaling arguments based on the equilibrium polymer size fail ... [J. Chem. Phys. 133, 044904 (2010)] published Tue Jul 27, 2010.

Molecular dynamics of natural rubber as revealed by dielectric spectroscopy: The role of natural crosslinking

Javier CarreteroGonzalez, Tiberio A. Ezquerra, Sureerut Amnuaypornsri, Shigeyuki Toki, Raquel Verdejo et al.
In order to understand the molecular dynamics of natural rubber, the dielectric relaxation behavior of its different components were investigated. These components included: (1) the linear polyisoprene fraction, obtained after deproteinization and transesterification of natural rubber (TEDPNR), (2) ... [Soft Matter 6, 3636 ] published .

Properties of knotted ring polymers. I. Equilibrium dimensions

Marc L. Mansfield and Jack F. Douglas
We report calculations on three classes of knotted ring polymers: (1) simple-cubic lattice self-avoiding rings (SARs), (2) true theta-state rings, i.e., SARs generated on the simple-cubic lattice with an attractive nearest-neighbor contact potential (theta-SARs), and (3) ideal, Gaussian rings. Extra ... [J. Chem. Phys. 133, 044903 (2010)] published Tue Jul 27, 2010.

Reptation of a semiflexible polymer through porous media

Gimoon Nam, Albert Johner, and Nam-Kyung Lee
We study the motion of a single stiff semiflexible filament of length S through an array of topological obstacles. By means of scaling arguments and two-dimensional computer simulations, we show that the stiff chain kinetics follows the reptation picture, albeit with kinetic exponents (for the centr ... [J. Chem. Phys. 133, 044908 (2010)] published Fri Jul 30, 2010.

Dipolar sticky hard spheres within the PercusYevick approximation plus orientational linearization

Domenico Gazzillo
We consider a strongly idealized model for polar fluids, which consists of spherical particles, having, in addition to a hard-core repulsion, a surface dipolar interaction, acting only when particles are exactly at contact. A fully analytic solution of the molecular OrsteinZernike equation is found ... [J. Chem. Phys. 133, 034511 (2010)] published Tue Jul 20, 2010.

Void nucleation and disentanglement in glassy amorphous polymers

Dhiraj K. Mahajan, Bhupinder Singh, and Sumit Basu
Cavitation in glassy polymers is known to result from highly triaxial states of local stress and the presence of impurities. Understanding of cavitation, particularly void nucleation, is important as cavities are precursors to crazes, which in turn lead to fracture. In this work we study the early s ... [Phys. Rev. E 82, 011803 ] published .

Molecular dynamics simulations of glassy polymers

Jean-Louis Barrat, Jorg Baschnagel, and Alexey Lyulin
We review recent results from computer simulation studies of polymer glasses, from the chain dynamics around the glass transition temperature T to the mechanical behaviour below T. These results clearly show that modern computer simulations are able to address and give clear answers to some importan ... [Soft Matter 6, 3430 ] published .

Energetics and electronic structure of phenyl-disubstituted polyacetylene: A first-principles study

Priya Sony, Alok Shukla, and Claudia Ambrosch-Draxl
Phenyl-disubstituted polyacetylene (PDPA) is an organic semiconductor which has been studied during recent years for its efficient photoluminescence. In contrast, the molecular geometry, providing the basis for the electronic and optical properties has been hardly investigated. In this paper, we app ... [Phys. Rev. B 82, 035213 ] published .

Molecular dynamics simulations of polymer crystallization in highly supercooled melt: Primary nucleation and cold crystallization

Takashi Yamamoto
Molecular mechanisms of crystallization at large supercooling and structure of supercooled melt are investigated in our polyethylenelike polymer through molecular dynamics simulations. Three representative crystallization processes are here considered: (1) isothermal homogeneous nucleation in the me ... [J. Chem. Phys. 133, 034904 (2010)] published Tue Jul 20, 2010.

Giant Electrorheological Effect: A Microscopic Mechanism

Shuyu Chen, Xianxiang Huang, Nico F. A. van der Vegt, Weijia Wen, and Ping Sheng
Electrorheological fluids constitute a type of colloids that can vary their rheological characteristics upon the application of an electric field. The recently discovered giant electrorheological (GER) effect breaks the upper bound of the traditional ER effect, but a microscopic explanation is still ... [Phys. Rev. Lett. 105, 046001 ] published .

Polymer translocation through alpha-hemolysin pore with tunable polymer-pore electrostatic interaction

Chiu Tai Andrew Wong and M. Muthukumar
We have measured the ionic current blockages produced by single molecules of sodium poly(styrene sulfonate) passing through an alpha-hemolysin protein pore under an electric field. Most of the blockage events were composed of one or two blockage levels of ionic current. By analyzing the statistics o ... [J. Chem. Phys. 133, 045101 (2010)] published Fri Jul 23, 2010.

Liquid crystal models of biological materials and processes

Alejandro D. Rey
This paper presents an overview of liquid crystal (LC) models of phase diagrams, phase transitions, self-assembly, interfaces, defects, and rheology and their integrated applications to biological mesophase materials and processes. Biological liquid crystals, classified into analogues (helicoidal pl ... [Soft Matter 6, 3402 ] published .

Fluorescence imaging of membrane dynamics in living cells

Petra Weber, Michael Wagner, and Herbert Schneckenburger
Methods of wide-field fluorescence microscopy for measuring membrane dynamics of living cells are described, including spectral imaging as well as anisotropy imaging of the membrane marker 6-dodecanoyl-2-dimethylamino naphthalene (laurdan). Plasma membranes are selected by illumination with an evane ... [J. Biomed. Opt. 15, 046017 (2010)] published Thu Jul 29, 2010.

Theoretical investigation of shear stress generated by a contrast microbubble on the cell membrane as a mechanism for sonoporation

Alexander A. Doinikov and Ayache Bouakaz
There are numerous experimental investigations on sonoporation, while the theoretical background of this phenomenon still is in its infancy. One of the suggested mechanisms of sonoporation is linked to shear stress exerted on the cell membrane by acoustic microstreaming generated by a contrast micro ... [J. Acoust. Soc. Am. 128, 11 (2010)] published Fri Jul 16, 2010.

Law of Mass Action, Detailed Balance, and the Modeling of Calcium Puffs

S. Rudiger, J. W. Shuai, and I. M. Sokolov
Using deterministic-stochastic simulations we show that for intracellular calcium puffs the mixing assumption for reactants does not hold within clusters of receptor channels. Consequently, the law of mass action does not apply and useful definitions of averaged calcium concentrations in the cluster ... [Phys. Rev. Lett. 105, 048103 ] published .

LRRC26 auxiliary protein allows BK channel activation at resting voltage without calcium

Jiusheng Yan and Richard W. Aldrich
Large-conductance, voltage- and calcium-activated potassium (BK, or K1.1) channels are ubiquitously expressed in electrically excitable and non-excitable cells, either as -subunit (BK) tetramers or together with tissue specific auxiliary -subunits (14). Activation of BK channels typically requires ... [Nature 466, 513 (2010)] published Thu Jul 22, 2010.

Model for the orientational ordering of the plant microtubule cortical array

Rhoda J. Hawkins, Simon H. Tindemans, and Bela M. Mulder
The plant microtubule cortical array is a striking feature of all growing plant cells. It consists of a more or less homogeneously distributed array of highly aligned microtubules connected to the inner side of the plasma membrane and oriented transversely to the cell growth axis. Here, we formulate ... [Phys. Rev. E 82, 011911 ] published .

Luminescent vesicular receptors for the recognition of biologically important phosphate species

Benjamin Gruber, Stefan Stadlbauer, Kristina Woinaroschy, and Burkhard Konig
The anion binding ability of bis-zinc cyclen complexes in buffered aqueous solution was investigated using indicator displacement assays (IDA) as well as luminescent labelled complexes. A high affinity to phosphate anions, such as UTP or pyrophosphate was observed in IDA while there was no observabl ... [Org. Biomol. Chem. 8, 3704 (2010)] published Thu Jul 29, 2010.

The hydrogen bond network structure within the hydration shell around simple osmolytes: Urea, tetramethylurea, and trimethylamine-N-oxide, investigated using both a fixed charge and a polarizable water model

Anna Kuffel and Jan Zielkiewicz
Despite numerous experimental and computer simulation studies, a controversy still exists regarding the effect of osmolytes on the structure of surrounding water. There is a question, to what extent some of the contradictory results may arise from differences in potential models used to simulate the ... [J. Chem. Phys. 133, 035102 (2010)] published Mon Jul 19, 2010.

Water filling of hydrophilic nanopores

Ezequiel de la Llave, Valeria Molinero, and Damian A. Scherlis
Molecular dynamics simulations of water in cylindrical hydrophilic pores with diameters of 1.5 and 3 nm were performed to explore the phase behavior and the nucleation dynamics of the confined fluid as a function of the percentage of volume filled f. The interactions of water with the pore wall were ... [J. Chem. Phys. 133, 034513 (2010)] published Wed Jul 21, 2010.

Accurate calculations of the hydration free energies of druglike molecules using the reference interaction site model

David S. Palmer, Volodymyr P. Sergiievskyi, Frank Jensen, and Maxim V. Fedorov
We report on the results of testing the reference interaction site model (RISM) for the estimation of the hydration free energy of druglike molecules. The optimum model was selected after testing of different RISM free energy expressions combined with different quantum mechanics and empirical force- ... [J. Chem. Phys. 133, 044104 (2010)] published Thu Jul 22, 2010.

Spectroscopic elucidation of uncoupled transition energies in the major photosynthetic light-harvesting complex, LHCII

Gabriela S. Schlau-Cohen, Tessa R. Calhoun, Naomi S. Ginsberg, Matteo Ballottari, Roberto Bassi et al.
Electrostatic couplings between chromophores in photosynthetic pigmentprotein complexes, and interactions of pigments with the surrounding protein environment, produce a complicated energy landscape of delocalized excited states. The resultant electronic structure absorbs light and gives rise to en ... [Proc. Natl. Acad. Sci. U.S.A. 107, 13276 (2010)] published Wed Jul 28, 2010.

DFT calculations on the deprotonation site of the one-electron oxidised guaninecytosine base pair

Steen Steenken and Johannes Reynisson
As calculated by the density functional theory (DFT), the acidity of cytosine's exocyclic amine group (CNH) in the base pair GC is considerably increased upon its one-electron oxidation. The proton affinity (PA) of the amine moiety is lowered by ionisation of GC (which yields GC) from -348.1 to -269 ... [Phys. Chem. Chem. Phys. 12, 9088 (2010)] published Thu Jul 29, 2010.

Long-lived quantum coherence in photosynthetic complexes at physiological temperature

Gitt Panitchayangkoon, Dugan Hayes, Kelly A. Fransted, Justin R. Caram, Elad Harel et al.
Photosynthetic antenna complexes capture and concentrate solar radiation by transferring the excitation to the reaction center that stores energy from the photon in chemical bonds. This process occurs with near-perfect quantum efficiency. Recent experiments at cryogenic temperatures have revealed t ... [Proc. Natl. Acad. Sci. U.S.A. 107, 12766 (2010)] published Mon Jul 26, 2010.

Erratum: Bimolecular reaction rates from ring polymer molecular dynamics [J. Chem. Phys. 130, 174713 (2009)]

Rosana Collepardo-Guevara, Yury V. Suleimanov, and David E. Manolopoulos
Abstract not available. [J. Chem. Phys. 133, 049902 (2010)] published Fri Jul 30, 2010.

Efficient Simulation of Strong System-Environment Interactions

Javier Prior, Alex W. Chin, Susana F. Huelga, and Martin B. Plenio
Multicomponent quantum systems in strong interaction with their environment are receiving increasing attention due to their importance in a variety of contexts, ranging from solid state quantum information processing to the quantum dynamics of biomolecular aggregates. Unfortunately, these systems ar ... [Phys. Rev. Lett. 105, 050404 ] published .

How in the 20th century physicists, chemists and biologists answered the question: what is life?

Valentin Reutov and A Schechter
The most essential achievements in 20th century biology are analyzed and the question of how throughout the last century physicists, chemists and biologists answered the question "What is life?" is considered. The most considerable scientific achievement of 20th century biology, and perhaps of all ... [Phys.-Usp. 53, 377 (2010)] published Wed Jul 28, 2010.

New Opportunities for an Ancient Material

Fiorenzo G. Omenetto and David L. Kaplan
Spiders and silkworms generate silk protein fibers that embody strength and beauty. Orb webs are fascinating feats of bioengineering in nature, displaying magnificent architectures while providing essential survival utility for spiders. The unusual combination of high strength and extensibility is a ... [Science 329, 528 ] published .

21st century: what is life from the perspective of physics?

Genrikh Ivanitskii
The evolution of the biophysical paradigm over 65 years since the publication in 1944 of Erwin Schrodinger's What is Life? The Physical Aspects of the Living Cell is reviewed. Based on the advances in molecular genetics, it is argued that all the features characteristic of living systems can also b ... [Phys.-Usp. 53, 327 (2010)] published Wed Jul 28, 2010.

Nonlinear dynamics of the brain: emotion and cognition

Mikhail Rabinovich and M Muezzinoglu
Experimental investigations of neural system functioning and brain activity are standardly based on the assumption that perceptions, emotions, and cognitive functions can be understood by analyzing steady-state neural processes and static tomographic snapshots. The new approaches discussed in this ... [Phys.-Usp. 53, 357 (2010)] published Wed Jul 28, 2010.