Virtual Journal of Biological Physics Research

Construction and operation of a microrobot based on magnetotactic bacteria in a microfluidic chip

Qiufeng Ma, Changyou Chen, Shufeng Wei, Chuanfang Chen, Long-Fei Wu et al.
Magnetotactic bacteria (MTB) are capable of swimming along magnetic field lines. This unique feature renders them suitable in the development of magnetic-guided, auto-propelled microrobots to serve in target molecule separation and detection, drug delivery, or target cell screening in a microfluidic ... [Biomicrofluidics 6, 024107 (2012)] published Tue Apr 10, 2012.

Optical trapping force reduction and manipulation of nanoporous beads

Tao Wang, Fan Jiang, Stefan Oehrlein, Erliang Zeng, Ryan Kershner et al.
We studied the interaction of infrared optical traps with controlled-pore glass (CPG) beads in aqueous medium. The lateral optical trapping force and stiffness were experimentally found considerably smaller than those of their solid counterparts. The simulation using an average refractive index reve ... [Appl. Phys. Lett. 100, 153702 (2012)] published Wed Apr 11, 2012.

High-throughput genotoxicity assay identifies antioxidants as inducers of DNA damage response and cell death

Jennifer T. Fox, Srilatha Sakamuru, Ruili Huang, Nedelina Teneva, Steven O. Simmons et al.
Human ATAD5 is a biomarker for identifying genotoxic compounds because ATAD5 protein levels increase posttranscriptionally in response to DNA damage. We screened over 4,000 compounds with a cell-based quantitative high-throughput ATAD5-luciferase assay detecting genotoxic compounds. We identified 2 ... [Proc. Natl. Acad. Sci. U.S.A. 109, 5423 (2012)] published Tue Apr 3, 2012.

Direct Electrochemistry and Electrocatalysis of Hemoglobin Immobilized on the Functionalized Graphene-Carbon Nanotube Composite Film

Minzhi Wang and Jianbin Zheng
The direct electrochemistry of hemoglobin (Hb) immobilized on the designed carboxyl functionalized polystyrene/graphene-carbon nanotube-Nafion modified indium tin oxide (PS/GE-CNT-Nafion/ITO) electrode and its electrocatalysis for hydrogen peroxide (HO) were investigated. UV-visible and Fourier-tran ... [J. Electrochem. Soc. 159, F150 (2012)] published Wed Apr 4, 2012.

Determination of single cell surface protein expression using a tagless microfluidic method

Rajan Kumar, Sri HariKrishna Vellanki, Robin Smith, and Robert Wieder
We describe a method to detect the expression of a surface protein in single cells without prior labeling or manipulation using a microfluidic device. When the protein is expressed on a cell surface, it undergoes transient bond formation with an immobilized ligand as the cell is pumped through a mic ... [Lab Chip 12, 1646 (2012)] published Thu Apr 5, 2012.

Inhibiting protein biofouling using graphene oxide in droplet-based microfluidic microsystems

Guillaume Perry, Vincent Thomy, Manash R. Das, Yannick Coffinier, and Rabah Boukherroub
Biofouling or adsorption of biomolecules onto surfaces in microfluidic devices limits the type of samples which can be handled. In this paper, we take advantage of the high adsorption capacity of graphene oxide (GO) for proteins as a strategy to limit biofouling, while preserving their activity for ... [Lab Chip 12, 1601 (2012)] published Thu Apr 5, 2012.

Spectral analysis of fundamental signal and noise performances in photoconductors for mammography

Ho Kyung Kim, Chang Hwy Lim, Jesse Tanguay, Seungman Yun, and Ian A. Cunningham
Purpose: This study investigates the fundamental signal and noise performance limitations imposed by the stochastic nature of x-ray interactions in selected photoconductor materials, such as Si, a-Se, CdZnTe, HgI, PbI, PbO, and TlBr, for x-ray spectra typically used in mammography.Methods: It is sho ... [Med. Phys. 39, 2478 (2012)] published Fri Apr 13, 2012.

A miniaturized and integrated gel post platform for multiparameter PCR detection of herpes simplex viruses from raw genital swabs

Dammika P. Manage, Jana Lauzon, Alexey Atrazhev, Yuen C. Morrissey, Ann L. Edwards et al.
Herpes simplex virus (HSV) is one of the most prevalent viruses, with acute and recurrent infections in humans. The current gold standard for the diagnosis of HSV is viral culture which takes 214 days and has low sensitivity. In contrast, DNA amplification by polymerase chain reaction (PCR) can be p ... [Lab Chip 12, 1664 (2012)] published Thu Apr 5, 2012.

On-bead expression of recombinant proteins in an agarose gel matrix coated on a glass slide

Kyung-Ho Lee, Ka-Young Lee, Ju-Young Byun, Byung-Gee Kim, and Dong-Myung Kim
A system for expression and in situ display of recombinant proteins on a microbead surface is described. Biotinylated PCR products were immobilized on microbead surfaces, which were then embedded in a gel matrix and supplied with translation machinery and substrates. Upon the incubation of the gel m ... [Lab Chip 12, 1605 (2012)] published Thu Apr 5, 2012.

Ultrafast Rotary PCR system for multiple influenza viral RNA detection

Jae Hwan Jung, Seok Jin Choi, Byung Hyun Park, Young Ki Choi, and Tae Seok Seo
We presented a novel platform for an ultrafast PCR system, called the Rotary PCR Genetic Analyzer, which incorporates a thermal block and resistive temperature detector (RTD) for thermal cycling control, a disposable PCR microchip, and a stepper motor. The influenza viral RNAs from H3N2, H5N1, and H ... [Lab Chip 12, 1598 (2012)] published Thu Apr 5, 2012.

Anisotropic light scattering of individual sickle red blood cells

Youngchan Kim, John M. Higgins, Ramachandra R. Dasari, Subra Suresh, and YongKeun Park
We present the anisotropic light scattering of individual red blood cells (RBCs) from a patient with sickle cell disease (SCD). To measure light scattering spectra along two independent axes of elongated-shaped sickle RBCs with arbitrary orientation, we introduce the anisotropic Fourier transform li ... [J. Biomed. Opt. 17, 040501 (2012)] published Tue Apr 3, 2012.

Development of a microbial high-throughput screening instrument based on elastic light scatter patterns

Euiwon Bae, Valery Patsekin, Bartek Rajwa, Arun K. Bhunia, Cheryl Holdman et al.
A microbial high-throughput screening (HTS) system was developed that enabled high-speed combinatorial studies directly on bacterial colonies. The system consists of a forward scatterometer for elastic light scatter (ELS) detection, a plate transporter for sample handling, and a robotic incubator fo ... [Rev. Sci. Instrum. 83, 044304 (2012)] published Thu Apr 12, 2012.

A three-lead, programmable, and microcontroller-based electrocardiogram generator with frequency domain characteristics of heart rate variability

Ying-Chieh Wei, Ying-Yu Wei, Kai-Hsiung Chang, and Ming-Shing Young
The objective of this study is to design and develop a programmable electrocardiogram (ECG) generator with frequency domain characteristics of heart rate variability (HRV) which can be used to test the efficiency of ECG algorithms and to calibrate and maintain ECG equipment. We simplified and modifi ... [Rev. Sci. Instrum. 83, 045109 (2012)] published Mon Apr 9, 2012.

Continuous-waveform constant-current isolated physiological stimulator

Mark R. Holcomb, Jack M. Devine, Rene Harder, and Veniamin Y. Sidorov
We have developed an isolated continuous-waveform constant-current physiological stimulator that is powered and controlled by universal serial bus (USB) interface. The stimulator is composed of a custom printed circuit board (PCB), 16-MHz MSP430F2618 microcontroller with two integrated 12-bit digita ... [Rev. Sci. Instrum. 83, 044303 (2012)] published Fri Apr 6, 2012.

A new device for performing reference point indentation without a reference probe

Daniel Bridges, Connor Randall, and Paul K. Hansma
Here we describe a novel, hand-held reference point indentation (RPI), instrument that is designed for clinical measurements of bone material properties in living patients. This instrument differs from previous RPI instruments in that it requires neither a reference probe nor removal of the perioste ... [Rev. Sci. Instrum. 83, 044301 (2012)] published Wed Apr 4, 2012.

Possible use of a Cooper-pair box for low-dose electron microscopy

Hiroshi Okamoto
A transmission electron microscope that takes advantage of superconducting quantum circuitry is proposed. The microscope is designed to improve the image contrast of radiation-sensitive weak-phase objects, in particular, biological specimens. The objective in this setting is to measure the phase shi ... [Phys. Rev. A 85, 043810 ] published .

Squeeze-chip: a finger-controlled microfluidic flow network device and its application to biochemical assays

Wentao Li, Tao Chen, Zitian Chen, Peng Fei, Zhilong Yu et al.
We designed and fabricated a novel microfluidic device that can be operated through simple finger squeezing. On-chip microfluidic flow control is enabled through an optimized network of check-valves and squeeze-pumps. The sophisticated flow system can be easily constructed by combining a few key ele ... [Lab Chip 12, 1587 (2012)] published Thu Apr 5, 2012.

Error analysis of ratiometric imaging of extracellular pH in a window chamber model

Yuxiang Lin, Tzu-Yu Wu, and Arthur F. Gmitro
Ratiometric fluorescence-imaging technique is commonly used to measure extracellular pH in tumors and surrounding tissue within a dorsal skin-fold window chamber. Using a pH-sensitive fluorophore such as carboxy SNARF-1 one can measure pH distributions with high precision. However, it is often obser ... [J. Biomed. Opt. 17, 046004 (2012)] published Thu Apr 5, 2012.

The microwave sensing of DNA hybridization using carbon nanotubes decorated with gold nanoislands

Alina Cismaru, Mircea Dragoman, Antonio Radoi, A. Dinescu, and Daniela Dragoman
The hybridization of the deoxyribonucleic acid (DNA) is detected with the help of electromagnetic band gap resonator. The resonance frequency of the unloaded resonator f=16.07 GHz is shifted to the left at 11.49 GHz when the resonator is loaded with single-stranded DNA anchored to gold nanoislands d ... [J. Appl. Phys. 111, 076106 (2012)] published Fri Apr 13, 2012.

Covalently immobilized biomolecule gradient on hydrogel surface using a gradient generating microfluidic device for a quantitative mesenchymal stem cell study

Zongbin Liu, Lidan Xiao, Baojian Xu, Yu Zhang, Arthur FT Mak et al.
Precisely controlling the spatial distribution of biomolecules on biomaterial surface is important for directing cellular activities in the controlled cell microenvironment. This paper describes a polydimethylsiloxane (PDMS) gradient-generating microfluidic device to immobilize the gradient of cellu ... [Biomicrofluidics 6, 024111 (2012)] published Fri Apr 13, 2012.

Microstripes for transport and separation of magnetic particles

Marco Donolato, Bjarke Thomas Dalslet, and Mikkel Fougt Hansen
We present a simple technique for creating an on-chip magnetic particle conveyor based on exchange-biased permalloy microstripes. The particle transportation relies on an array of stripes with a spacing smaller than their width in conjunction with a periodic sequence of four different externally app ... [Biomicrofluidics 6, 024110 (2012)] published Fri Apr 13, 2012.

High-performance microfluidic rectifier based on sudden expansion channel with embedded block structure

Chien-Hsiung Tsai, Che-Hsin Lin, Lung-Ming Fu, and Hui-Chun Chen
A high-performance microfluidic rectifier incorporating a microchannel and a sudden expansion channel is proposed. In the proposed device, a block structure embedded within the expansion channel is used to induce two vortex structures at the end of the microchannel under reverse flow conditions. The ... [Biomicrofluidics 6, 024108 (2012)] published Fri Apr 13, 2012.

Dielectrophoretic differentiation of mouse ovarian surface epithelial cells, macrophages, and fibroblasts using contactless dielectrophoresis

Alireza Salmanzadeh, Harsha Kittur, Michael B. Sano, Paul C. Roberts, Eva M. Schmelz et al.
Ovarian cancer is the leading cause of death from gynecological malignancies in women. The primary challenge is the detection of the cancer at an early stage, since this drastically increases the survival rate. In this study we investigated the dielectrophoretic responses of progressive stages of mo ... [Biomicrofluidics 6, 024104 (2012)] published Tue Apr 3, 2012.

Novel on-demand droplet generation for selective fluid sample extraction

Robert Lin, Jeffery S. Fisher, Melinda G. Simon, and Abraham P. Lee
A novel microfluidic device enabling selective generation of droplets and encapsulation of targets is presented. Unlike conventional methods, the presented mechanism generates droplets with unique selectivity by utilizing a K-junction design. The K-junction is a modified version of the classic T-jun ... [Biomicrofluidics 6, 024103 (2012)] published Tue Apr 3, 2012.

New rationale for large metazoan embryo manipulations on chip-based devices

Khashayar Khoshmanesh, Jin Akagi, Chris J. Hall, Kathryn E. Crosier, Philip S. Crosier et al.
The lack of technologies that combine automated manipulation, sorting, as well as immobilization of single metazoan embryos remains the key obstacle to high-throughput organism-based ecotoxicological analysis and drug screening routines. Noticeably, the major obstacle hampering the automated trappin ... [Biomicrofluidics 6, 024102 (2012)] published Tue Apr 3, 2012.

Field-free particle focusing in microfluidic plugs

G. K. Kurup and Amar S. Basu
Particle concentration is a key unit operation in biochemical assays. Although there are many techniques for particle concentration in continuous-phase microfluidics, relatively few are available in multiphase (plug-based) microfluidics. Existing approaches generally require external electric or mag ... [Biomicrofluidics 6, 022008 (2012)] published Wed Apr 11, 2012.

Tunable spatial heterogeneity in structure and composition within aqueous microfluidic droplets

Su Hui Sophia Lee, Pengzhi Wang, Swee Kun Yap, T. Alan Hatton, and Saif A. Khan
In this paper, we demonstrate biphasic microfluidic droplets with broadly tunable internal structures, from simple near-equilibrium drop-in-drop morphologies to complex yet uniform non-equilibrium steady-state structures. The droplets contain an aqueous mixture of poly(ethylene glycol) (PEG) and dex ... [Biomicrofluidics 6, 022005 (2012)] published Fri Apr 6, 2012.

Tuning bubbly structures in microchannels

Sharon M. Vuong and Shelley L. Anna
Foams have many useful applications that arise from the structure and size distribution of the bubbles within them. Microfluidics allows for the rapid formation of uniform bubbles, where bubble size and volume fraction are functions of the input gas pressure, liquid flow rate, and device geometry. A ... [Biomicrofluidics 6, 022004 (2012)] published Fri Apr 6, 2012.

CO dissolution in water using long serpentine microchannels

Thomas Cubaud, Martin Sauzade, and Ruopeng Sun
The evolution of carbon dioxide bubbles dissolving in water is experimentally examined using long microchannels. We study the coupling between bubble hydrodynamics and dissolution in confined geometries. The gas impregnation process in liquid produces significant flow rearrangements. Depending on th ... [Biomicrofluidics 6, 022002 (2012)] published Fri Apr 6, 2012.

Calcium carbonate polymorph control using droplet-based microfluidics

Alexandra Yashina, Fiona Meldrum, and Andrew deMello
Calcium carbonate (CaCO) is one of the most abundant minerals and of high importance in many areas of science including global CO exchange, industrial water treatment energy storage, and the formation of shells and skeletons. Industrially, calcium carbonate is also used in the production of cement, ... [Biomicrofluidics 6, 022001 (2012)] published Fri Apr 6, 2012.

Handheld magnetic sensor for measurement of tension

K. Singal and R. Rajamani
This letter develops an analytical formulation for measurement of tension in a string using a handheld sensor. By gently pushing the sensor against the string, the tension in the string can be obtained. An experimental sensor prototype is constructed to verify the analytical formulation. The centime ... [Appl. Phys. Lett. 100, 154105 (2012)] published Thu Apr 12, 2012.

Pico calorimeter for detection of heat produced in an individual brown fat cell

Naoki Inomata, Masaya Toda, Masaaki Sato, Akihiko Ishijima, and Takahito Ono
A pico calorimeter with a highly sensitive sensor for detecting heat from a biological cell is developed and evaluated, and also the heat detection of a single brown fat cell has been demonstrated. The measurement principle relies on resonant frequency tracking of a resonator in temperature variatio ... [Appl. Phys. Lett. 100, 154104 (2012)] published Tue Apr 10, 2012.

Vibrational frequencies of anti-diabetic drug studied by terahertz time-domain spectroscopy

S. Q. Du, H. Li, L. Xie, L. Chen, Y. Peng et al.
By using terahertz time-domain spectroscopy, the absorption spectra of seven anti-diabetic pills have been investigated. For gliquidone, glipizide, gliclazide, and glimepiride, an obvious resonance peak is found at 1.37 THz. Furthermore, to overcome the limit of density functional theory that can an ... [Appl. Phys. Lett. 100, 143702 (2012)] published Tue Apr 3, 2012.

Proposal for tunnel-field-effect-transistor as ultra-sensitive and label-free biosensors

Deblina Sarkar and Kaustav Banerjee
Tunnel field-effect-transistor (TFET) based biosensor is proposed, and it is shown that they can surpass by several orders, the performance of those based on conventional FET (CFET) and hence, can potentially revolutionize the biosensing applications. Analytical formula is derived for the sensitivit ... [Appl. Phys. Lett. 100, 143108 (2012)] published Thu Apr 5, 2012.

The double-helix microscope super-resolves extended biological structures by localizing single blinking molecules in three dimensions with nanoscale precision

Hsiao-lu D. Lee, Steffen J. Sahl, Matthew D. Lew, and W. E. Moerner
The double-helix point spread function microscope encodes the axial (z) position information of single emitters in wide-field (x,y) images, thus enabling localization in three dimensions (3D) inside extended volumes. We experimentally determine the statistical localization precision sigma of this ap ... [Appl. Phys. Lett. 100, 153701 (2012)] published Mon Apr 9, 2012.

Electrokinetic effects on detection time of nanowire biosensor

Yaling Liu, Qingjiang Guo, Shunqiang Wang, and Walter Hu
We develop a multiphysics model to study the contribution of electrokinetics on the biomolecular detection process and provide a physical explanation of the two to three orders of magnitude difference in detection time between experimental results and theoretical predications at ultralow concentrati ... [Appl. Phys. Lett. 100, 153502 (2012)] published Mon Apr 9, 2012.

Fano resonance in two-intersecting nanorings: Multiple layers of plasmon hybridizations

Hailong Liu, Xijun Wu, Bing Li, Chenxi Xu, Guangbiao Zhang et al.
We theoretically investigate the optical properties of two-intersecting nanorings (TINR), which exhibit a pronounced Fano resonance in the near-infrared region. A multiple-layer plasmon hybridization model is proposed to explain the reasons and forming processes of the Fano resonance. The dependence ... [Appl. Phys. Lett. 100, 153114 (2012)] published Wed Apr 11, 2012.

Correlations between ultrasonic guided wave velocities and bone properties in bovine tibia in vitro

Kang Il Lee and Suk Wang Yoon
Correlations between ultrasonic guided wave velocities and bone properties were investigated in bovine tibia in vitro. The velocities of the first arriving signal and the slow guided wave, termed V and V, along the long axis of the tibia were measured at 200 kHz in 20 bovine tibiae using the axial t ... [J. Acoust. Soc. Am. 131, EL375 (2012)] published Mon Apr 9, 2012.

Cantilever deflection associated with hybridization of monomolecular DNA film

Yue Zhao, Baskar Ganapathysubramanian, and Pranav Shrotriya
Recent experiments show that specific binding between a ligand and surface immobilized receptor, such as hybridization of single stranded DNA immobilized on a microcantilever surface, leads to cantilever deflection. The binding-induced deflection may be used as a method for detection of biomolecules ... [J. Appl. Phys. 111, 074310 (2012)] published Fri Apr 6, 2012.

Micro-patterned porous substrates for cell-based assays

Fanny Evenou, Jean-Marc Di Meglio, Benoit Ladoux, and Pascal Hersen
In the search for new therapeutic chemicals, lab-on-a-chip systems have recently emerged as innovative and efficient tools for cell-based assays and high throughput screening. Here, we describe a novel, versatile and simple device for cell-based assays at the bench-top. We created spatial variations ... [Lab Chip 12, 1717 (2012)] published Thu Apr 5, 2012.

Performance and scaling effects in a multilayer microfluidic extracorporeal lung oxygenation device

Tatiana Kniazeva, Alla A. Epshteyn, James C. Hsiao, Ernest S. Kim, Vijaya B. Kolachalama et al.
Microfluidic fabrication technologies are emerging as viable platforms for extracorporeal lung assist devices and oxygenators for cardiac surgical support and critical care medicine, based in part on their ability to more closely mimic the architecture of the human vasculature than existing technolo ... [Lab Chip 12, 1686 (2012)] published Thu Apr 5, 2012.

Note: Multiplexed multiple-tau auto- and cross-correlators on a single field programmable gate array

G. Mocsar, B. Kreith, J. Buchholz, J. W. Krieger, J. Langowski et al.
We introduce a new multiple-tau hardware correlator design for computing fluorescence correlation functions (CFs) in real time. Use of hardware resources is minimized by scheduling the computation of different segments of the CFs on a single correlator block. Simultaneous calculation of two multiple ... [Rev. Sci. Instrum. 83, 046101 (2012)] published Wed Apr 4, 2012.

A thermal study of cellular motility by optical time-resolved correlation

F. J. Sierra-Valdez, A. J. Cisneros-Mejorado, D. P. Sanchez Herrera, and J. C. Ruiz-Suarez
The study of motor properties of cells under appropriate physical-chemical conditions is a significant problem nowadays. The standard techniques presently used do not allow to evaluate neither large samples nor to control their thermodynamic conditions. In this work, we report a cell motility sensor ... [Rev. Sci. Instrum. 83, 044302 (2012)] published Wed Apr 4, 2012.

Functionalized electrospun nanofibers as bioseparators in microfluidic systems

Lauren Matlock-Colangelo, Daehwan Cho, Christine L. Pitner, Margaret W. Frey, and Antje J. Baeumner
Functionalized electrospun nanofibers were integrated into microfluidic channels to serve as on-chip bioseparators. Specifically, poly(vinyl alcohol) (PVA) nanofiber mats were shown to successfully serve as bioseparators for negatively charged nanoparticles. Nanofibers were electrospun onto gold mic ... [Lab Chip 12, 1696 (2012)] published Thu Apr 5, 2012.

Two-Dimensional X-Ray Beam Phase Sensing

Sebastien Berujon, Eric Ziegler, Roberto Cerbino, and Luca Peverini
We present a new method to analyze quantitatively the wave front of a partially coherent x-ray beam. The technique is based on the use of two-dimensional speckle patterns combined with digital image correlation algorithms and offers a pixel size resolution, a high accuracy, and a reduced sensitivity ... [Phys. Rev. Lett. 108, 158102 ] published .

Supercontinuum ultra wide range confocal microscope for reflectance spectroscopy of living matter and material science surfaces

Stefano Selci, Francesca R. Bertani, and Luisa Ferrari
We report the design and implementation of a new reflectance laser scanning confocal system with spectroscopy imaging capabilities. Confocal spectroscopy is achieved by using a very broad spectral range supercontinuum source capable of high precision reflectance data in the VIS-IR spectral range tha ... [AIP Advances 1, 032143 (2011)] published Thu Aug 18, 2011.

Stereoscopic full aperture imaging in nuclear medicine

Sergio G. Strocovsky and Dino Otero
Images of planar scintigraphy and single photon emission computerized tomography (SPECT) used in nuclear medicine are often low quality. They usually appear to be blurred and noisy. This problem is due to the low spatial resolution and poor sensitivity of the acquisition technique with the gamma cam ... [AIP Advances 1, 022121 (2011)] published Tue May 24, 2011.

Gold nanoparticle wire and integrated wire array for electronic detection of chemical and biological molecules

J. J. Diao and Qing Cao
Nanoparticle wire and integrated nanoparticle wire array have been prepared through a green technique: discontinuous vertical evaporation-driven colloidal deposition. The conducting gold nanoparticle wire made by this technique shows ability for the sensitive electronic detection of chemical and bio ... [AIP Advances 1, 012115 (2011)] published Wed Mar 30, 2011.

Time-lapse two-color 3D imaging of live cells with doubled resolution using structured illumination

Reto Fiolka, Lin Shao, E. Hesper Rego, Michael W. Davidson, and Mats G. L. Gustafsson
Previous implementations of structured-illumination microscopy (SIM) were slow or designed for one-color excitation, sacrificing two unique and extremely beneficial aspects of light microscopy: live-cell imaging in multiple colors. This is especially unfortunate because, among the resolution-extend ... [Proc. Natl. Acad. Sci. U.S.A. 109, 5311 (2012)] published Tue Apr 3, 2012.

Fluorescent graphene oxide composites synthesis and its biocompatibility study

Guoqiang Xie, Ju Cheng, Yifan Li, Pinxian Xi, Fengjuan Chen et al.
In this research, we developed a clean and wet route to produce sandwich-like fluorescent CdQ/GO composites sheets starting from graphene oxide (GO) and Cd in water/ethanol solution in one pot. The as-prepared CdQ/GO composites sheets were fully characterized by IR, XRD, TEM and TGA analysis. The Cd ... [J. Mater. Chem. 22, 9308 (2012)] published Thu Apr 12, 2012.

Linear conversion of pressure into concentration, rapid switching of concentration, and generation of linear ramps of concentration in a microfluidic device

Micha Adler and Alex Groisman
Mixing of liquids to produce solutions with different concentrations is one of the basic functionalities of microfluidic devices. Generation of specific temporal patterns of concentration in microfluidic devices is an important technique to study responses of cells and model organisms to variations ... [Biomicrofluidics 6, 024109 (2012)] published Fri Apr 13, 2012.

A controlled biochemical release device with embedded nanofluidic channels

Haifeng Yang, Wei Hong, and Liang Dong
A controlled release device is developed by embedding nanofluidic biomolecule reservoirs into a polymer network of a stimuli-responsive hydrogel. The reservoirs are made of liquid core-polymer shell nanofibers using co-electrospinning. The mechanism of controlled release is based on buckling instabi ... [Appl. Phys. Lett. 100, 153510 (2012)] published Fri Apr 13, 2012.

Covalent attachment of a specific site of a protein molecule on a carbon nanotube tip

Hiroyuki Maruyama, Shige H. Yoshimura, Satoshi Ohno, Kazuya Nishikawa, and Yoshikazu Nakayama
We have demonstrated the attachment of a specific site of importin alpha protein molecules to carbon nanotube (CNT) tips. A specific site of importin alpha was labeled with an artificial amino acid: azidotyrosine. Using the Staudinger reaction, the specific reaction between azide groups and a triary ... [J. Appl. Phys. 111, 074701 (2012)] published Tue Apr 3, 2012.

Rapid crystallization from acoustically levitated droplets

Hui-Ling Cao, Da-Chuan Yin, Yun-Zhu Guo, Xiao-Liang Ma, Jin He et al.
This paper reports on an ultrasonic levitation system developed for crystallization from solution in a containerless condition. The system has been proven to be able to levitate droplets stably and grow crystals rapidly and freely from a levitated droplet. Crystals of four samples, including NaCl, N ... [J. Acoust. Soc. Am. 131, 3164 (2012)] published Thu Apr 12, 2012.

Fluorescence microscopy for simultaneous observation of 3D orientation and movement and its application to quantum rod-tagged myosin V

Masashi Ohmachi, Yasunori Komori, Atsuko H. Iwane, Fumihiko Fujii, Takashi Jin et al.
Single molecule fluorescence polarization techniques have been used for three-dimensional (3D) orientation measurements to observe the dynamic properties of single molecules. However, only few techniques can simultaneously measure 3D orientation and position. Furthermore, these techniques often req ... [Proc. Natl. Acad. Sci. U.S.A. 109, 5294 (2012)] published Tue Apr 3, 2012.

Hollow YPO:Eu microspheres: synthesis, characterisation and luminescent properties

Hongfang Jiu, Yuehua Fu, Lixin Zhang, Yixin Sun, Yuanzhong Wang et al.
YPO:Eu hollow microspheres were synthesised by using the spheres of PS/Y(OH)CO:Eu as a precursor. The whole process mainly consists of the hydrothermal reaction and calcination. The YPO:Eu hollow spheres were characterised by X-ray diffraction, scanning electron microscopy, transmission electron mic ... [Micro Nano Lett. 7, 287 (2012)] published Tue Apr 3, 2012.

Physics of ultra-high bioproductivity in algal photobioreactors

Efrat Greenwald, Jeffrey M. Gordon, and Yair Zarmi
Cultivating algae at high densities in thin photobioreactors engenders time scales for random cell motion that approach photosynthetic rate-limiting time scales. This synchronization allows bioproductivity above that achieved with conventional strategies. We show that a diffusion model for cell moti ... [Appl. Phys. Lett. 100, 143703 (2012)] published Wed Apr 4, 2012.

A microfluidic platform for controlled biochemical stimulation of twin neuronal networks

Emilia Biffi, Francesco Piraino, Alessandra Pedrocchi, Gianfranco B. Fiore, Giancarlo Ferrigno et al.
Spatially and temporally resolved delivery of soluble factors is a key feature for pharmacological applications. In this framework, microfluidics coupled to multisite electrophysiology offers great advantages in neuropharmacology and toxicology. In this work, a microfluidic device for biochemical st ... [Biomicrofluidics 6, 024106 (2012)] published Tue Apr 3, 2012.

Development of formaldehyde-free agar/gelatin microcapsules containing berberine HCl and gallic acid and their topical and oral applications

Pik-Ling Lam, Kenneth Ka-Ho Lee, Stanton Hon-Lung Kok, Gregory Yin-Ming Cheng, Xiao-Ming Tao et al.
The safety issues of biomedical applications have been a major concern in recent years. Drug delivery associated with microencapsulation technology has been focused on as microencapsulated drugs are believed to promote comparative therapeutic efficiency on human absorption and prolong the life cycle ... [Soft Matter 8, 5027 (2012)] published Thu Apr 12, 2012.

Using feature vectors to detect frog calls in wireless sensor networks

Benjamin Croker and Navinda Kottege
A method for detecting vocalization of giant barred frogs (Mixophyes iteratus) in noisy audio is proposed. Audio recordings from remote wireless sensor nodes were segmented into individual sounds and from each sound a small set of features was extracted. Feature vectors were compared to those of exa ... [J. Acoust. Soc. Am. 131, EL400 (2012)] published Fri Apr 13, 2012.

Conjugated polyelectrolyte complexes with single-walled carbon nanotubes for amperometric detection of glucose with inherent anti-interference properties

Xin Pang, Patigul Imin, Igor Zhitomirsky, and Alex Adronov
Supramolecular complexes between single-walled carbon nanotubes and the conjugated polyelectrolytes poly[3-(3-N,N-diethylaminopropoxy)thiophene] (PDAOT), poly[3-(3[prime]-thienyloxy)propanesulfonate] (P3TOPS), and poly[2,5-bis(3-sulfonatopropoxy)-1,4-ethynylphenylene-alt-1,4-ethynylphenylene] (aPPE) ... [J. Mater. Chem. 22, 9147 (2012)] published Thu Apr 12, 2012.

Biocompatible and functionalizable polyphosphate nanogel with a branched structure

You-Yong Yuan, Jin-Zhi Du, Wen-Jing Song, Feng Wang, Xian-Zhu Yang et al.
Biocompatible and biodegradable nanogels with a branched structure designed as potential carriers for drug delivery are reported here. The nanogels were prepared by the reaction of 3,6-dioxaoctan-1,8-diyl bis(ethylene phosphate) (TEGDP) with tris(2-aminoethyl)amine (TREN) in an ionic liquid containi ... [J. Mater. Chem. 22, 9322 (2012)] published Thu Apr 12, 2012.

Improved delay-leaping simulation algorithm for biochemical reaction systems with delays

Na Yi, Gang Zhuang, Liang Da, and Yifei Wang
In biochemical reaction systems dominated by delays, the simulation speed of the stochastic simulation algorithm depends on the size of the wait queue. As a result, it is important to control the size of the wait queue to improve the efficiency of the simulation. An improved accelerated delay stocha ... [J. Chem. Phys. 136, 144108 (2012)] published Wed Apr 11, 2012.

Oscillation death in asymmetrically delay-coupled oscillators

Wei Zou, Yang Tang, Lixiang Li, and Jurgen Kurths
Symmetrically coupled oscillators represent a limiting case for studying the dynamics of natural systems. Therefore, we here investigate the effect of coupling asymmetry on delay-induced oscillation death (OD) in coupled nonlinear oscillators. It is found that the asymmetrical coupling substantially ... [Phys. Rev. E 85, 046206 ] published .

Time-varying linear and nonlinear parametric model for Granger causality analysis

Yang Li, Hua-Liang Wei, Steve A. Billings, and Xiao-Feng Liao
Statistical measures such as coherence, mutual information, or correlation are usually applied to evaluate the interactions between two or more signals. However, these methods cannot distinguish directions of flow between two signals. The capability to detect causalities is highly desirable for unde ... [Phys. Rev. E 85, 041906 ] published .

Noise-sustained fluctuations in stochastic dynamics with a delay

Paolo D'Odorico, Francesco Laio, and Luca Ridolfi
Delayed responses to external drivers are ubiquitous in environmental, social, and biological processes. Delays may induce oscillations, Hopf bifurcations, and instabilities in deterministic systems even in the absence of nonlinearities. Despite recent advances in the study of delayed stochastic dif ... [Phys. Rev. E 85, 041106 ] published .

Testing for time-localized coherence in bivariate data

L. W. Sheppard, A. Stefanovska, and P. V. E. McClintock
We present a method for the testing of significance when evaluating the coherence of two oscillatory time series that may have variable amplitude and frequency. It is based on evaluating the self-correlations of the time series. We demonstrate our approach by the application of wavelet-based coheren ... [Phys. Rev. E 85, 046205 ] published .

Hydrodynamic synchronization of nonlinear oscillators at low Reynolds number

M. Leoni and T. B. Liverpool
We introduce a generic model of a weakly nonlinear self-sustained oscillator as a simplified tool to study synchronization in a fluid at low Reynolds number. By averaging over the fast degrees of freedom, we examine the effect of hydrodynamic interactions on the slow dynamics of two oscillators and ... [Phys. Rev. E 85, 040901 ] published .

Stochastic dynamics of phase singularities under ventricular fibrillation in 2D Beeler-Reuter model

Akio Suzuki and Hidetoshi Konno
The dynamics of ventricular fibrillation (VF) has been studied extensively, and the initiation mechanism of VF has been elucidated to some extent. However, the stochastic dynamical nature of sustained VF remains unclear so far due to the complexity of high dimensional chaos in a heterogeneous system ... [AIP Advances 1, 032103 (2011)] published Mon Jul 18, 2011.

Langevin dynamics simulation of polymer-assisted virus-like assembly

J. P. Mahalik and M. Muthukumar
Starting from a coarse grained representation of the building units of the minute virus of mice and a flexible polyelectrolyte molecule, we have explored the mechanism of assembly into icosahedral structures with the help of Langevin dynamics simulations and the parallel tempering technique. Regular ... [J. Chem. Phys. 136, 135101 (2012)] published Mon Apr 2, 2012.

Footprint traversal by adenosine-triphosphate-dependent chromatin remodeler motor

Ashok Garai, Jesrael Mani, and Debashish Chowdhury
Adenosine-triphosphate (ATP)-dependent chromatin remodeling enzymes (CREs) are biomolecular motors in eukaryotic cells. These are driven by a chemical fuel, namely, ATP. CREs actively participate in many cellular processes that require accessibility of specific segments of DNA which are packaged as ... [Phys. Rev. E 85, 041902 ] published .

Adiabatically slow and adiabatically fast driven ratchets

V. M. Rozenbaum, Yu. A. Makhnovskii, I. V. Shapochkina, S.-Y. Sheu, D.-Y. Yang et al.
We revisit two known models of deterministically driven ratchets, which exhibit high energetic efficiency, with the goal to uncover similarities and differences in the principles of their operation. Both the models rely on adiabaticity of the potential change process, however, the adiabaticity that ... [Phys. Rev. E 85, 041116 ] published .

Reaction-diffusion master equation in the microscopic limit

Stefan Hellander, Andreas Hellander, and Linda Petzold
Stochastic modeling of reaction-diffusion kinetics has emerged as a powerful theoretical tool in the study of biochemical reaction networks. Two frequently employed models are the particle-tracking Smoluchowski framework and the on-lattice reaction-diffusion master equation (RDME) framework. As the ... [Phys. Rev. E 85, 042901 ] published .

Non-Brownian dynamics and strategy of amoeboid cell locomotion

Shin I. Nishimura, Masahiro Ueda, and Masaki Sasai
Amoeboid cells such as Dictyostelium discoideum and Madin-Darby canine kidney cells show the non-Brownian dynamics of migration characterized by the superdiffusive increase of mean-squared displacement. In order to elucidate the physical mechanism of this non-Brownian dynamics, a computational model ... [Phys. Rev. E 85, 041909 ] published .

A universal model for mobility and migration patterns

Filippo Simini, Marta C. Gonzlez, Amos Maritan, and Albert-Lszl Barabsi
Introduced in its contemporary form in 1946 (ref. 1), but with roots that go back to the eighteenth century, the gravity law is the prevailing framework with which to predict population movement, cargo shipping volume and inter-city phone calls, as well as bilateral trade flows between nations. Des ... [Nature 484, 96 (2012)] published Thu Apr 5, 2012.

Origin of first cells at terrestrial, anoxic geothermal fields

Armen Y. Mulkidjanian, Andrew Yu. Bychkov, Daria V. Dibrova, Michael Y. Galperin, and Eugene V. Koonin
All cells contain much more potassium, phosphate, and transition metals than modern (or reconstructed primeval) oceans, lakes, or rivers. Cells maintain ion gradients by using sophisticated, energy-dependent membrane enzymes (membrane pumps) that are embedded in elaborate ion-tight membranes. The f ... [Proc. Natl. Acad. Sci. U.S.A. 109, E821 (2012)] published Tue Apr 3, 2012.

Effect of space in the game war of attrition

Philip Gerlee and Torbjorn Lundh
Spatial dynamics has in many cases been invoked as a mechanism that can promote the evolution of coexistence and cooperation, although the precise conditions for this to occur have not yet been characterised. In an effort to address this question we have analyzed an alternative version of the theore ... [Phys. Rev. E 85, 041115 ] published .

Accelerating consensus on coevolving networks: The effect of committed individuals

P. Singh, S. Sreenivasan, B. K. Szymanski, and G. Korniss
Social networks are not static but, rather, constantly evolve in time. One of the elements thought to drive the evolution of social network structure is homophilythe need for individuals to connect with others who are similar to them. In this paper, we study how the spread of a new opinion, idea, or ... [Phys. Rev. E 85, 046104 ] published .

Topological analysis of complexity in multiagent systems

Nicole Abaid, Erik Bollt, and Maurizio Porfiri
Social organisms at every level of evolutionary complexity live in groups, such as fish schools, locust swarms, and bird flocks. The complex exchange of multifaceted information across group members may result in a spectrum of salient spatiotemporal patterns characterizing collective behaviors. Whil ... [Phys. Rev. E 85, 041907 ] published .

Emergence of Fairness in Repeated Group Interactions

S. Van Segbroeck, J. M. Pacheco, T. Lenaerts, and F. C. Santos
Often groups need to meet repeatedly before a decision is reached. Hence, most individual decisions will be contingent on decisions taken previously by others. In particular, the decision to cooperate or not will depend on one's own assessment of what constitutes a fair group outcome. Making use of ... [Phys. Rev. Lett. 108, 158104 ] published .

Vertebrate time-tree elucidates the biogeographic pattern of a major biotic change around the KT boundary in Madagascar

Angelica Crottini, Ole Madsen, Celine Poux, Axel Strauss, David R. Vieites et al.
The geographic and temporal origins of Madagascar's biota have long been in the center of debate. We reconstructed a time-tree including nearly all native nonflying and nonmarine vertebrate clades present on the island, from DNA sequences of two single-copy protein-coding nuclear genes (BDNF and RA ... [Proc. Natl. Acad. Sci. U.S.A. 109, 5358 (2012)] published Tue Apr 3, 2012.

Evolutionary Dynamics of Restriction Site Avoidance

Long Qian and Edo Kussell
Molecular noise in bacterial restriction-modification systems can cause rare events of host DNA cleavage at restriction sites. Such noise-induced selective pressure may result in evolved sequences exhibiting restriction site avoidance. We identify a two-state regime of evolutionary dynamics, in whic ... [Phys. Rev. Lett. 108, 158105 ] published .

Stochastic differential equations for evolutionary dynamics with demographic noise and mutations

Arne Traulsen, Jens Christian Claussen, and Christoph Hauert
We present a general framework to describe the evolutionary dynamics of an arbitrary number of types in finite populations based on stochastic differential equations (SDEs). For large, but finite populations this allows us to include demographic noise without requiring explicit simulations. Instead, ... [Phys. Rev. E 85, 041901 ] published .

The genomic basis of adaptive evolution in threespine sticklebacks

Felicity C. Jones, Manfred G. Grabherr, Yingguang Frank Chan, Pamela Russell, Evan Mauceli et al.
Marine stickleback fish have colonized and adapted to thousands of streams and lakes formed since the last ice age, providing an exceptional opportunity to characterize genomic mechanisms underlying repeated ecological adaptation in nature. Here we develop a high-quality reference genome assembly fo ... [Nature 484, 55 (2012)] published Thu Apr 5, 2012.

Protein misinteraction avoidance causes highly expressed proteins to evolve slowly

Jian-Rong Yang, Ben-Yang Liao, Shi-Mei Zhuang, and Jianzhi Zhang
The tempo and mode of protein evolution have been central questions in biology. Genomic data have shown a strong influence of the expression level of a protein on its rate of sequence evolution (E-R anticorrelation), which is currently explained by the protein misfolding avoidance hypothesis. Here, ... [Proc. Natl. Acad. Sci. U.S.A. 109, E831 (2012)] published Tue Apr 3, 2012.

Mixed lineage kinase domain-like is a key receptor interacting protein 3 downstream component of TNF-induced necrosis

Jie Zhao, Siriporn Jitkaew, Zhenyu Cai, Swati Choksi, Qiuning Li et al.
Tumor necrosis factor (TNF) is an important inflammatory cytokine and induces many cellular responses, including inflammation, cell proliferation, apoptosis, and necrosis. It is known that receptor interacting protein (RIP) kinases, RIP1 and RIP3, are key effectors of TNF-induced necrosis, but litt ... [Proc. Natl. Acad. Sci. U.S.A. 109, 5322 (2012)] published Tue Apr 3, 2012.

Dense PEG layers for efficient immunotargeting of nanoparticles to cancer cells

Benjamin Thierry and Hans J. Griesser
In order to achieve a high density of grafted PEG chains on functional nanoparticles, a 2-step method is proposed that enables the tethering of the PEG chains under theta solvency conditions while preserving their colloidal stability. UV-vis studies were first used to determine the phase transition ... [J. Mater. Chem. 22, 8810 (2012)] published Thu Apr 12, 2012.

Atg7 Modulates p53 Activity to Regulate Cell Cycle and Survival During Metabolic Stress

In Hye Lee, Yoshichika Kawai, Maria M. Fergusson, Ilsa I. Rovira, Alexander J. R. Bishop et al.
Withdrawal of nutrients triggers an exit from the cell division cycle, the induction of autophagy, and eventually the activation of cell death pathways. The relation, if any, among these events is not well characterized. We found that starved mouse embryonic fibroblasts lacking the essential autopha ... [Science 336, 225 (2012)] published Wed Apr 11, 2012.

Monitoring of tumor response to cisplatin by subsurface fluorescence molecular tomography

Fei Liu, Xu Cao, Wei He, Jinping Song, Zhongquan Dai et al.
Subsurface fluorescence molecular tomography (FMT) has promising potential for noninvasive characterization of molecular and cellular activities in small animals by tomographic means in reflectance geometry. In this work, subsurface FMT is employed to monitor the therapeutic response of cisplatin in ... [J. Biomed. Opt. 17, 040504 (2012)] published Mon Apr 9, 2012.

Notch-dependent VEGFR3 upregulation allows angiogenesis without VEGFVEGFR2 signalling

Rui Benedito, Susana F. Rocha, Marina Woeste, Martin Zamykal, Freddy Radtke et al.
Developing tissues and growing tumours produce vascular endothelial growth factors (VEGFs), leading to the activation of the corresponding receptors in endothelial cells. The resultant angiogenic expansion of the local vasculature can promote physiological and pathological growth processes. Previou ... [Nature 484, 110 (2012)] published Thu Apr 5, 2012.

Multiphoton microscopy and microspectroscopy for diagnostics of inflammatory and neoplastic lung

Ina Pavlova, Kelly R. Hume, Stephanie A. Yazinski, James Flanders, Teresa L. Southard et al.
Limitations of current medical procedures for detecting early lung cancers inspire the need for new diagnostic imaging modalities for the direct microscopic visualization of lung nodules. Multiphoton microscopy (MPM) provides for subcellular resolution imaging of intrinsic fluorescence from unproces ... [J. Biomed. Opt. 17, 036014 (2012)] published Tue Apr 3, 2012.

Comparative analysis of nonlinear dimensionality reduction techniques for breast MRI segmentation

Alireza Akhbardeh and Michael A. Jacobs
Purpose: Visualization of anatomical structures using radiological imaging methods is an important tool in medicine to differentiate normal from pathological tissue and can generate large amounts of data for a radiologist to read. Integrating these large data sets is difficult and time-consuming. A ... [Med. Phys. 39, 2275 (2012)] published Tue Apr 3, 2012.

Tumor-binding prodrug micelles of polymerdrug conjugates for anticancer therapy in HeLa cells

Bokyung Jung, Yong-Cheol Jeong, Jun-Hong Min, Jung-Eun Kim, Yoon-Jae Song et al.
An interesting phytosphingosine (PHS), a natural sphingolipid metabolite comprising ceramides, is believed to play a vital role in strong anticancer therapeutic efficacy for various types of cancer cells, which is based on a programmed cellular death mechanism, so called apoptosis. However, extremel ... [J. Mater. Chem. 22, 9385 (2012)] published Thu Apr 12, 2012.

Paclitaxel-loaded tocopheryl succinate-conjugated chitosan oligosaccharide nanoparticles for synergistic chemotherapy

Youhua Tao, Jianfeng Han, and Huanyu Dou
Although countless work on the synthesis, encapsulation and toxicity of paclitaxel-loaded nanoparticles (NPs) has been reported, there have been few reports on the development of the nano-carrier materials of the paclitaxel (PTX) delivery system with therapeutic effects. In this study, we synthesize ... [J. Mater. Chem. 22, 8930 (2012)] published Thu Apr 12, 2012.

A Fine-Scale Chimpanzee Genetic Map from Population Sequencing

Adam Auton, Adi Fledel-Alon, Susanne Pfeifer, Oliver Venn, Laure Sgurel et al.
To study the evolution of recombination rates in apes, we developed methodology to construct a fine-scale genetic map from high-throughput sequence data from 10 Western chimpanzees, Pan troglodytes verus. Compared to the human genetic map, broad-scale recombination rates tend to be conserved, but wi ... [Science 336, 193 (2012)] published Wed Apr 11, 2012.

Extrachromosomal MicroDNAs and Chromosomal Microdeletions in Normal Tissues

Yoshiyuki Shibata, Pankaj Kumar, Ryan Layer, Smaranda Willcox, Jeffrey R. Gagan et al.
We have identified tens of thousands of short extrachromosomal circular DNAs (microDNA) in mouse tissues as well as mouse and human cell lines. These microDNAs are 200 to 400 base pairs long, are derived from unique nonrepetitive sequence, and are enriched in the 5[prime]-untranslated regions of gen ... [Science 336, 82 (2012)] published Tue Apr 3, 2012.

Maternal siRNAs as regulators of parental genome imbalance and gene expression in endosperm of Arabidopsis seeds

Jie Lu, Changqing Zhang, David C. Baulcombe, and Z. Jeffrey Chen
Seed size is important to crop domestication and natural selection and is affected by the balance of maternal and paternal genomes in endosperm. Endosperm, like placenta in mammals, provides reserves to the developing embryo. Interploidy crosses disrupt the genome balance in endosperm and alter see ... [Proc. Natl. Acad. Sci. U.S.A. 109, 5529 (2012)] published Tue Apr 3, 2012.

Optimizing information flow in small genetic networks. III. A self-interacting gene

Gasper TkaCik, Aleksandra M. Walczak, and William Bialek
Living cells must control the reading out or expression of information encoded in their genomes, and this regulation often is mediated by transcription factorsproteins that bind to DNA and either enhance or repress the expression of nearby genes. But the expression of transcription factor proteins i ... [Phys. Rev. E 85, 041903 ] published .

Genome-wide proteinDNA binding dynamics suggest a molecular clutch for transcription factor function

Colin R. Lickwar, Florian Mueller, Sean E. Hanlon, James G. McNally, and Jason D. Lieb
Dynamic access to genetic information is central to organismal development and environmental response. Consequently, genomic processes must be regulated by mechanisms that alter genome function relatively rapidly. Conventional chromatin immunoprecipitation (ChIP) experiments measure transcription f ... [Nature 484, 251 (2012)] published Thu Apr 12, 2012.

DNA damage defines sites of recurrent chromosomal translocations in B lymphocytes

Ofir Hakim, Wolfgang Resch, Arito Yamane, Isaac Klein, Kyong-Rim Kieffer-Kwon et al.
Recurrent chromosomal translocations underlie both haematopoietic and solid tumours. Their origin has been ascribed to selection of random rearrangements, targeted DNA damage, or frequent nuclear interactions between translocation partners; however, the relative contribution of each of these element ... [Nature 484, 69 (2012)] published Thu Apr 5, 2012.

Population Genomics of Early Events in the Ecological Differentiation of Bacteria

B. Jesse Shapiro, Jonathan Friedman, Otto X. Cordero, Sarah P. Preheim, Sonia C. Timberlake et al.
Genetic exchange is common among bacteria, but its effect on population diversity during ecological differentiation remains controversial. A fundamental question is whether advantageous mutations lead to selection of clonal genomes or, as in sexual eukaryotes, sweep through populations on their own. ... [Science 336, 48 (2012)] published Tue Apr 3, 2012.

Stochastic stability of genetic regulatory networks with a finite set delay characterization

Wenbing Zhang, Yang Tang, Jian-an Fang, and Xiaotai Wu
In this paper, the delay-distribution-dependent stability is derived for the stochastic genetic regulatory networks (GRNs) with a finite set delay characterization and interval parameter uncertainties. One important feature of the obtained results here is that the time-varying delays are assumed to ... [Chaos 22, 023106 (2012)] published Thu Apr 12, 2012.

Emergence of robustness against noise: A structural phase transition in evolved models of gene regulatory networks

Tiago P. Peixoto
We investigate the evolution of Boolean networks subject to a selective pressure which favors robustness against noise, as a model of evolved genetic regulatory systems. By mapping the evolutionary process into a statistical ensemble and minimizing its associated free energy, we find the structural ... [Phys. Rev. E 85, 041908 ] published .

Choice-specific sequences in parietal cortex during a virtual-navigation decision task

Christopher D. Harvey, Philip Coen, and David W. Tank
The posterior parietal cortex (PPC) has an important role in many cognitive behaviours; however, the neural circuit dynamics underlying PPC function are not well understood. Here we optically imaged the spatial and temporal activity patterns of neuronal populations in mice performing a PPC-dependent ... [Nature 484, 62 (2012)] published Thu Apr 5, 2012.

Mapping the Core of the Arabidopsis Circadian Clock Defines the Network Structure of the Oscillator

W. Huang, P. Prez-Garca, A. Pokhilko, A. J. Millar, I. Antoshechkin et al.
In many organisms, the circadian clock is composed of functionally coupled morning and evening oscillators. In Arabidopsis, oscillator coupling relies on a core loop in which the evening oscillator component TIMING OF CAB EXPRESSION 1 (TOC1) was proposed to activate a subset of morning-expressed osc ... [Science 336, 75 (2012)] published Tue Apr 3, 2012.

Coordination of the transcriptome and metabolome by the circadian clock

Kristin L. Eckel-Mahan, Vishal R. Patel, Robert P. Mohney, Katie S. Vignola, Pierre Baldi et al.
The circadian clock governs a large array of physiological functions through the transcriptional control of a significant fraction of the genome. Disruption of the clock leads to metabolic disorders, including obesity and diabetes. As food is a potent zeitgeber (ZT) for peripheral clocks, metabolit ... [Proc. Natl. Acad. Sci. U.S.A. 109, 5541 (2012)] published Tue Apr 3, 2012.

Bistability and Spatiotemporal Irregularity in Neuronal Networks with Nonlinear Synaptic Transmission

Gianluigi Mongillo, David Hansel, and Carl van Vreeswijk
We present a mean-field theory for spiking networks operating in the balanced excitation-inhibition regime, with synapses displaying short-term plasticity. The theory reveals a novel mechanism for bistability which relies on the nonlinearity of the synaptic interactions. As synaptic nonlinearity is ... [Phys. Rev. Lett. 108, 158101 ] published .

Neutral theory of chemical reaction networks

Sang Lee, Sebastian Bernhardsson, Petter Holme, Beom Kim, and Petter Minnhagen
To what extent do the characteristic features of a chemical reaction network reflect its purpose and function? In general, one argues that correlations between specific features and specific functions are key to understanding a complex structure. However, specific features may sometimes be neutral a ... [New J. Phys. 14, 033032 (2012)] published Tue Apr 3, 2012.

Analytical framework for recurrence network analysis of time series

Jonathan F. Donges, Jobst Heitzig, Reik V. Donner, and Jurgen Kurths
Recurrence networks are a powerful nonlinear tool for time series analysis of complex dynamical systems. While there are already many successful applications ranging from medicine to paleoclimatology, a solid theoretical foundation of the method has still been missing so far. Here, we interpret an [ ... [Phys. Rev. E 85, 046105 ] published .

Tunable oscillations in the Purkinje neuron

Ze'ev R. Abrams, Ajithkumar Warrier, Yuan Wang, Dirk Trauner, and Xiang Zhang
In this paper, we experimentally study the dynamics of slow oscillations in Purkinje neurons in vitro, and derive a strong association with a forced parametric oscillator model. We observed the precise rhythmicity of these oscillations in Purkinje neurons, as well as a dynamic tunability of this osc ... [Phys. Rev. E 85, 041905 ] published .

Unbiased degree-preserving randomization of directed binary networks

E. S. Roberts and A. C. C. Coolen
Randomizing networks using a naive accept-all edge-swap algorithm is generally biased. Building on recent results for nondirected graphs, we construct an ergodic detailed balance Markov chain with nontrivial acceptance probabilities for directed graphs, which converges to a strictly uniform measure ... [Phys. Rev. E 85, 046103 ] published .

Neuronal avalanches of a self-organized neural network with active-neuron-dominant structure

Xiumin Li and Michael Small
Neuronal avalanche is a spontaneous neuronal activity which obeys a power-law distribution of population event sizes with an exponent of 3/2. It has been observed in the superficial layers of cortex both invivo and invitro. In this paper, we analyze the information transmission of a novel self-organ ... [Chaos 22, 023104 (2012)] published Wed Apr 11, 2012.

Wetting transitions of cellular aggregates induced by substrate rigidity

Stephane Douezan, Julien Dumond, and Francoise Brochard-Wyart
The inhibition of tissue spreading is of great interest for medical applications, including the prevention of tumor mass dispersal to avoid cancer propagation. While chemical approaches have previously been reported to control tissue spreading, here we investigate a physical mechanism to inhibit spr ... [Soft Matter 8, 4577 (2012)] published Thu Apr 5, 2012.

Quantitative correlation between light depolarization and transport albedo of various porcine tissues

Sanaz Alali, Manzoor Ahmad, Anthony Kim, Nasit Vurgun, Michael F. G. Wood et al.
We present a quantitative study of depolarization in biological tissues and correlate it with measured optical properties (reduced scattering and absorption coefficients). Polarized light imaging was used to examine optically thick samples of both isotropic (liver, kidney cortex, and brain) and anis ... [J. Biomed. Opt. 17, 045004 (2012)] published Mon Apr 9, 2012.

Cluster identification based on correlations

L. S. Schulman
The problem addressed is the identification of cooperating agents based on correlations created as a result of the joint action of these and other agents. A systematic method for using correlations beyond second moments is developed. The technique is applied to a didactic example, the identification ... [Phys. Rev. E 85, 041114 ] published .

Competitive Brownian and Levy walkers

E. Heinsalu, E. Hernandez-Garcia, and C. Lopez
Population dynamics of individuals undergoing birth and death and diffusing by short- or long-range two-dimensional spatial excursions (Gaussian jumps or Levy flights) is studied. Competitive interactions are considered in a global case, in which birth and death rates are influenced by all individua ... [Phys. Rev. E 85, 041105 ] published .

Method for physiologic phenotype characterization at the single-cell level in non-interacting and interacting cells

Laimonas Kelbauskas, Shashanka P. Ashili, Jeff Houkal, Dean Smith, Aida Mohammadreza et al.
Intercellular heterogeneity is a key factor in a variety of core cellular processes including proliferation, stimulus response, carcinogenesis, and drug resistance. However, cell-to-cell variability studies at the single-cell level have been hampered by the lack of enabling experimental techniques. ... [J. Biomed. Opt. 17, 037008 (2012)] published Tue Apr 3, 2012.

Scale-Invariant Correlations in Dynamic Bacterial Clusters

Xiao Chen, Xu Dong, Avraham Be'er, Harry L. Swinney, and H. P. Zhang
In Bacillus subtilis colonies, motile bacteria move collectively, spontaneously forming dynamic clusters. These bacterial clusters share similarities with other systems exhibiting polarized collective motion, such as bird flocks or fish schools. Here we study experimentally how velocity and orientat ... [Phys. Rev. Lett. 108, 148101 ] published .

A numerical analysis of multicellular environment for modeling tissue electroporation

M. Essone Mezeme, G. Pucihar, M. Pavlin, C. Brosseau, and D. MiklavCiC
Simulations probing the conductivity changes of three-dimensional models of biological tissues consisting of random ternary core-shell sphere packings with different spatial scales are described. We investigate the temporal evolution of the electric conductivity of these packings during application ... [Appl. Phys. Lett. 100, 143701 (2012)] published Tue Apr 3, 2012.

Critical Behavior and Axis Defining Symmetry Breaking in Hydra Embryonic Development

Andrea Gamba, Mario Nicodemi, Jordi Soriano, and Albrecht Ott
The formation of a hollow cellular sphere is often one of the first steps of multicellular embryonic development. In the case of Hydra, the sphere breaks its initial symmetry to form a foot-head axis. During this process a gene, ks1, is increasingly expressed in localized cell domains whose size dis ... [Phys. Rev. Lett. 108, 158103 ] published .

A new understanding of the decoding principle on the ribosome

Natalia Demeshkina, Lasse Jenner, Eric Westhof, Marat Yusupov, and Gulnara Yusupova
During protein synthesis, the ribosome accurately selects transfer RNAs (tRNAs) in accordance with the messenger RNA (mRNA) triplet in the decoding centre. tRNA selection is initiated by elongation factor Tu, which delivers tRNA to the aminoacyl tRNA-binding site (A site) and hydrolyses GTP upon es ... [Nature 484, 256 (2012)] published Thu Apr 12, 2012.

Adaptation at the output of the chemotaxis signalling pathway

Junhua Yuan, Richard W. Branch, Basarab G. Hosu, and Howard C. Berg
In the bacterial chemotaxis network, receptor clusters process input, and flagellar motors generate output. Receptor and motor complexes are coupled by the diffusible protein CheY-P. Receptor output (the steady-state concentration of CheY-P) varies from cell to cell. However, the motor is ultrasens ... [Nature 484, 233 (2012)] published Thu Apr 12, 2012.

Structure of TIGIT immunoreceptor bound to poliovirus receptor reveals a cellcell adhesion and signaling mechanism that requires cis-trans receptor clustering

Katharina F. Stengel, Kristin Harden-Bowles, Xin Yu, Lionel Rouge, Jianping Yin et al.
Nectins (nectin14) and Necls [nectin-like (Necl15)] are Ig superfamily cell adhesion molecules that regulate cell differentiation and tissue morphogenesis. Adherens junction formation and subsequent cellcell signaling is initiated by the assembly of higher-order receptor clusters of cognate molecul ... [Proc. Natl. Acad. Sci. U.S.A. 109, 5399 (2012)] published Tue Apr 3, 2012.

Structure of the mitotic checkpoint complex

William C. H. Chao, Kiran Kulkarni, Ziguo Zhang, Eric H. Kong, and David Barford
In mitosis, the spindle assembly checkpoint (SAC) ensures genome stability by delaying chromosome segregation until all sister chromatids have achieved bipolar attachment to the mitotic spindle. The SAC is imposed by the mitotic checkpoint complex (MCC), whose assembly is catalysed by unattached chr ... [Nature 484, 208 (2012)] published Thu Apr 12, 2012.

Designing orthogonal signaling pathways: How to fit in with the surroundings

John Karanicolas
Abstract not available. [Proc. Natl. Acad. Sci. U.S.A. 109, 5140 (2012)] published Tue Apr 3, 2012.

Control of protein signaling using a computationally designed GTPase/GEF orthogonal pair

Gregory T. Kapp, Sen Liu, Amelie Stein, Derek T. Wong, Attila Remenyi et al.
Signaling pathways depend on regulatory protein-protein interactions; controlling these interactions in cells has important applications for reengineering biological functions. As many regulatory proteins are modular, considerable progress in engineering signaling circuits has been made by recombin ... [Proc. Natl. Acad. Sci. U.S.A. 109, 5277 (2012)] published Tue Apr 3, 2012.

Experimental assessment of the contribution of electrodynamic interactions to long-distance recruitment of biomolecular partners: Theoretical basis

Jordane Preto, Elena Floriani, Ilaria Nardecchia, Pierre Ferrier, and Marco Pettini
Highly specific spatiotemporal interactions between cognate molecular partners essentially sustain all biochemical transactions in living matter. That such an exquisite level of accuracy may result from encountering forces solely driven by thermal diffusive processes is unlikely. Here we propose a y ... [Phys. Rev. E 85, 041904 ] published .

Carotenoid oxidation products are stress signals that mediate gene responses to singlet oxygen in plants

Fanny Ramel, Simona Birtic, Christian Ginies, Ludivine Soubigou-Taconnat, Christian Triantaphylides et al.
O (singlet oxygen) is a reactive O species produced from triplet excited chlorophylls in the chloroplasts, especially when plants are exposed to excess light energy. Similarly to other active O species, O has a dual effect: It is toxic, causing oxidation of biomolecules, and it can act as a signal ... [Proc. Natl. Acad. Sci. U.S.A. 109, 5535 (2012)] published Tue Apr 3, 2012.

Pathway switching in templated virus-like particle assembly

Irina Tsvetkova, Chao Chen, Subinoy Rana, C. Cheng Kao, Vincent M. Rotello et al.
Assembly pathways of virus-like particles formed from a virus coat protein cage encapsulating a metal nanoparticle were studied by intrinsic fluorescence quenching. Depending on buffer conditions, the in vitro formation of a virus-like particle can take place through cooperative or non-cooperative a ... [Soft Matter 8, 4570 (2012)] published Thu Apr 5, 2012.

Requirements for contractility in disordered cytoskeletal bundles

Martin Lenz, Margaret Gardel, and Aaron Dinner
Actomyosin contractility is essential for biological force generation, and is well understood in highly organized structures such as striated muscle. Additionally, actomyosin bundles devoid of this organization are known to contract both in vivo and in vitro, which cannot be described by standard mu ... [New J. Phys. 14, 033037 (2012)] published Tue Apr 3, 2012.

Nanoscale imaging of the bone cell network with synchrotron X-ray tomography: optimization of acquisition setup

Alexandra Pacureanu, Max Langer, Elodie Boller, Paul Tafforeau, and Francoise Peyrin
Purpose: The fundamental role of the osteocyte cell network in regulating the bone remodeling has become evident in the last years. This has raised the necessity to explore this complex three-dimensional interconnected structure, but the existing investigation methods cannot provide an adequate asse ... [Med. Phys. 39, 2229 (2012)] published Tue Apr 3, 2012.

MAP and kinesin-dependent nuclear positioning is required for skeletal muscle function

Thomas Metzger, Vincent Gache, Mu Xu, Bruno Cadot, Eric S. Folker et al.
The basic unit of skeletal muscle in all metazoans is the multinucleate myofibre, within which individual nuclei are regularly positioned. The molecular machinery responsible for myonuclear positioning is not known. Improperly positioned nuclei are a hallmark of numerous diseases of muscle, includi ... [Nature 484, 120 (2012)] published Thu Apr 5, 2012.

Bioactive silicapoly(gamma-glutamic acid) hybrids for bone regeneration: effect of covalent coupling on dissolution and mechanical properties and fabrication of porous scaffolds

G. Poologasundarampillai, B. Yu, O. Tsigkou, E. Valliant, S. Yue et al.
It is well known that bone has excellent mechanical properties through its hierarchical structure and that design of new materials should take inspiration from its structure, especially those that will be used as synthetic bone grafts. However it has not yet been possible to mimic the complex struct ... [Soft Matter 8, 4822 ] published .

Effect of erythrocytes oscillations on dielectric properties of human diabetic-blood

S. Abdalla
It has been demonstrated that the erythrocytes (RBCs) oscillate during their tank-treading motion with high-frequency oscillations. This oscillatory motion drastically affects the dielectric and electrical properties of RBCs. Moreover, the glucose level in blood affects the electrical and dielectric ... [AIP Advances 1, 012104 (2011)] published Wed Feb 16, 2011.

A method for tensile tests of biological tissues at the mesoscale

Thierry Savin, Amy E. Shyer, and L. Mahadevan
We describe a new technique for determining the tensile properties of biological tissues at the mesoscale. The procedure uses a calibrated magnetic interaction between a steel bead attached to the sample and a permanent magnet to apply a uniaxial tensile force, along with a simple video assay to mon ... [J. Appl. Phys. 111, 074704 (2012)] published Fri Apr 13, 2012.

Development of a theoretical model describing sonoporation activity of cells exposed to ultrasound in the presence of contrast agents

Monica M. Forbes and William D. O'Brien, Jr.
Sonoporation uses ultrasound, with the aid of ultrasound contrast agents (UCAs), to enhance cell permeabilization, thereby allowing delivery of therapeutic compounds noninvasively into specific target cells. The objective of this study was to determine if a computational model describing shear stres ... [J. Acoust. Soc. Am. 131, 2723 (2012)] published Thu Apr 12, 2012.

Long-distance correlations of rhinovirus capsid dynamics contribute to uncoating and antiviral activity

Amitava Roy and Carol Beth Post
Human rhinovirus (HRV) and other members of the enterovirus genus bind small-molecule antiviral compounds in a cavity buried within the viral capsid protein VP1. These compounds block the release of the viral protein VP4 and RNA from inside the capsid during the uncoating process. In addition, the ... [Proc. Natl. Acad. Sci. U.S.A. 109, 5271 (2012)] published Tue Apr 3, 2012.

Tensegrity and motor-driven effective interactions in a model cytoskeleton

Shenshen Wang and Peter G. Wolynes
Actomyosin networks are major structural components of the cell. They provide mechanical integrity and allow dynamic remodeling of eukaryotic cells, self-organizing into the diverse patterns essential for development. We provide a theoretical framework to investigate the intricate interplay between ... [J. Chem. Phys. 136, 145102 (2012)] published Thu Apr 12, 2012.

Self-assembly mechanisms of silk protein nanostructures on two-dimensional surfaces

Nicholas E. Kurland, Joydip Kundu, Shilpa Pal, Subhas C. Kundu, and Vamsi K. Yadavalli
Self-assembly processes are ubiquitous in natural systems, and their study can provide insight into the harnessing of unique properties for engineering of new materials from the bottom up. Models for diffusion-limited assembly behavior have shown that structures formed have a characteristic fractal ... [Soft Matter 8, 4952 (2012)] published Thu Apr 12, 2012.

Well-defined hydroxyapatitepolycation nanohybrids via surface-initiated atom transfer radical polymerization for biomedical applications

Q. Cai, Y. Zhu, J. Q. He, Z. H. Wang, Fabing Su et al.
The ability to manipulate and control the surface properties of hydroxyapatite (HA) nanoparticles is of crucial importance for the design of HA-based carriers of therapeutic agents. In this work, surface-initiated atom transfer radical polymerization (ATRP) of (2-dimethyl amino)ethyl methacrylate (D ... [J. Mater. Chem. 22, 9358 (2012)] published Thu Apr 12, 2012.

Mastered proteolysis of gelatin gel can control delivery kinetics of entrapped large molecules

Marie-Cecile Klak, Julien Picard, Sebastien Giraudier, and Veronique Larreta-Garde
Biogels are useful reservoirs for molecular delivery as they can entrap a large variety of compounds in their liquid phase. The delivery kinetics of these molecules is dictated by diffusion laws and thus depends on their molecular size. An original strategy to accelerate the release of large molecul ... [Soft Matter 8, 4749 (2012)] published Thu Apr 5, 2012.

Influence of adsorbed polyelectrolytes on pore size distribution of a water-swollen biomaterial

Niko Aarne, Eero Kontturi, and Janne Laine
Many biomaterials exhibit pronounced swelling and consequently pronounced porous structure when exposed to water. Characterization and tuning of the porosity are important for the fundamental understanding of the behaviour of the biomaterials as well as for many of their applications, both tradition ... [Soft Matter 8, 4739 (2012)] published Thu Apr 5, 2012.

Surface adhered poly(vinyl alcohol) physical hydrogels as tools for rational design of intelligent biointerfaces

Bettina E. B. Jensen, Marie-Helene Alves, Betina Fejerskov, Brigitte Stadler, and Alexander N. Zelikin
We develop three independent non-cryogenic techniques for the production of physical hydrogels based on poly(vinyl alcohol), PVA, as surface adhered materials. Hydrogelation of the micro-structured PVA films was achieved using a coagulating salt (sodium sulfate), aqueous isopropanol, and poly(ethyle ... [Soft Matter 8, 4624 (2012)] published Thu Apr 5, 2012.

Glycoconjugate-functionalized carbon nanotubes in biomedicine

Narasimha Murthy Bandaru and Nicolas Hans Voelcker
Carbon nanotubes (CNTs) are extensively explored in materials science for their mechanical, electronic, optical, and magnetic properties. In the biomedical domain, CNTs are enjoying increasing popularity as building blocks for novel drug delivery systems as well as for bioimaging and biosensing. The ... [J. Mater. Chem. 22, 8748 (2012)] published Thu Apr 12, 2012.

Polarization switching and patterning in self-assembled peptide tubular structures

Igor Bdikin, Vladimir Bystrov, Ivonne Delgadillo, Jose Gracio, Svitlana Kopyl et al.
Self-assembled peptide nanotubes are unique nanoscale objects that have great potential for a multitude of applications, including biosensors, nanotemplates, tissue engineering, biosurfactants, etc. The discovery of strong piezoactivity and polar properties in aromatic dipeptides [A. Kholkin, N. Amd ... [J. Appl. Phys. 111, 074104 (2012)] published Tue Apr 3, 2012.

Two independent switches regulate cytoplasmic dynein's processivity and directionality

Wilhelm J. Walter, Michael P. Koonce, Bernhard Brenner, and Walter Steffen
Cytoplasmic dynein is a microtubule-based molecular motor that participates in a multitude of cell activities, from cell division to organelle transport. Unlike kinesin and myosin, where different tasks are performed by highly specialized members of these superfamilies, a single form of the dynein ... [Proc. Natl. Acad. Sci. U.S.A. 109, 5289 (2012)] published Tue Apr 3, 2012.

Event distributions of polymer translocation

R. P. Linna and K. Kaski
We present event distributions for the polymer translocation obtained by extensive Langevin dynamics simulations. Such distributions have not been reported previously and they provide new understanding of the stochastic characteristics of the process. We extract at a high length scale resolution dis ... [Phys. Rev. E 85, 041910 ] published .

DNA with amphiphilic counterions: tuning colloidal DNA with cyclodextrin

Azat Bilalov, Jonas Carlstedt, Elena Krivtsova, Bjorn Lindman, and Ulf Olsson
DNA compaction in vitro can be controlled by lipids. Cyclodextrins can disperse lipids in the form of water soluble inclusion complexes, thus tuning their self-assembly. To progress in the fundamental understanding of double-stranded (ds) DNAlipidcyclodextrin interactions, the aqueous phase behavior ... [Soft Matter 8, 4988 (2012)] published Thu Apr 12, 2012.

Reading DNA at single-nucleotide resolution with a mutant MspA nanopore and phi29 DNA polymerase

Elizabeth A Manrao, Ian M Derrington, Andrew H Laszlo, Kyle W Langford, Matthew K Hopper et al.
Nanopore technologies are being developed for fast and direct sequencing of single DNA molecules through detection of ionic current modulations as DNA passes through a pore's constriction. Here we demonstrate the ability to resolve changes in current that correspond to a known DNA sequence by combi ... [Nature Biotechnol. 30, 349 (2012)] published Wed Apr 11, 2012.

Automated forward and reverse ratcheting of DNA in a nanopore at 5- precision

Gerald M Cherf, Kate R Lieberman, Hytham Rashid, Christopher E Lam, Kevin Karplus et al.
An emerging DNA sequencing technique uses protein or solid-state pores to analyze individual strands as they are driven in single-file order past a nanoscale sensor. However, uncontrolled electrophoresis of DNA through these nanopores is too fast for accurate base reads. Here, we describe forward a ... [Nature Biotechnol. 30, 344 (2012)] published Wed Apr 11, 2012.

An effective model of DNA like helicoidal structure: with length fluctuation nonlinearity

Y. M. Tseytlin
One of the natural helicoidal nanostructure, which thermomechanical features are studied carefully with the help of different mechanical models, is a DNA cell / molecule. Our study proves that the experimentally determined nonlinear fluctuations of the molecular length of DNA can be better understoo ... [AIP Advances 1, 012116 (2011)] published Wed Mar 30, 2011.

The geometrical origin of the strain-twist coupling in double helices

Kasper Olsen and Jakob Bohr
A simple geometrical explanation for the counterintuitive phenomenon when twist leads to extension in double helices is presented. The coupling between strain and twist is investigated using a tubular description. It is shown that the relation between strain and rotation is universal and depends onl ... [AIP Advances 1, 012108 (2011)] published Wed Feb 23, 2011.

Theory of binless multi-state free energy estimation with applications to protein-ligand binding

Zhiqiang Tan, Emilio Gallicchio, Mauro Lapelosa, and Ronald M. Levy
The weighted histogram analysis method (WHAM) is routinely used for computing free energies and expectations from multiple ensembles. Existing derivations of WHAM require observations to be discretized into a finite number of bins. Yet, WHAM formulas seem to hold even if the bin sizes are made arbit ... [J. Chem. Phys. 136, 144102 (2012)] published Mon Apr 9, 2012.

Fast relaxation and elasticity-related properties of trehalose-glycerol mixtures

Devin Averett, Marcus T. Cicerone, Jack F. Douglas, and Juan J. de Pablo
Molecular dynamics simulations are used to investigate basic fast relaxation properties and thermo-physical properties of trehalose-glycerol mixtures over a wide composition range and for a temperature range from above to below the glass transition temperature, T. An important aspect of the present ... [Soft Matter 8, 4936 (2012)] published Thu Apr 12, 2012.

Structure of the basal components of a bacterial transporter

Jeffrey Meisner, Tatsuya Maehigashi, Ingemar Andre, Christine M. Dunham, and Charles P. Moran
Proteins SpoIIQ and SpoIIIAH interact through two membranes to connect the forespore and the mother cell during endospore development in the bacterium Bacillus subtilis. SpoIIIAH consists of a transmembrane segment and an extracellular domain with similarity to YscJ proteins. YscJ proteins form lar ... [Proc. Natl. Acad. Sci. U.S.A. 109, 5446 (2012)] published Tue Apr 3, 2012.

Riboswitch control of Rho-dependent transcription termination

Kerry Hollands, Sergey Proshkin, Svetlana Sklyarova, Vitaly Epshtein, Alexander Mironov et al.
Riboswitches are RNA sensors that regulate gene expression upon binding specific metabolites or ions. Bacterial riboswitches control gene expression primarily by promoting intrinsic transcription termination or by inhibiting translation initiation. We now report a third general mechanism of riboswi ... [Proc. Natl. Acad. Sci. U.S.A. 109, 5376 (2012)] published Tue Apr 3, 2012.

Direct observation of multiple misfolding pathways in a single prion protein molecule

Hao Yu, Xia Liu, Krishna Neupane, Amar Nath Gupta, Angela M. Brigley et al.
Protein misfolding is a ubiquitous phenomenon associated with a wide range of diseases. Single-molecule approaches offer a powerful tool for deciphering the mechanisms of misfolding by measuring the conformational fluctuations of a protein with high sensitivity. We applied single-molecule force spe ... [Proc. Natl. Acad. Sci. U.S.A. 109, 5283 (2012)] published Tue Apr 3, 2012.

Using sketch-map coordinates to analyze and bias molecular dynamics simulations

Gareth A. Tribello, Michele Ceriotti, and Michele Parrinello
When examining complex problems, such as the folding of proteins, coarse grained descriptions of the system drive our investigation and help us to rationalize the results. Oftentimes collective variables (CVs), derived through some chemical intuition about the process of interest, serve this purpos ... [Proc. Natl. Acad. Sci. U.S.A. 109, 5196 (2012)] published Tue Apr 3, 2012.

Locating binding poses in protein-ligand systems using reconnaissance metadynamics

Par Soderhjelm, Gareth A. Tribello, and Michele Parrinello
A molecular dynamics-based protocol is proposed for finding and scoring protein-ligand binding poses. This protocol uses the recently developed reconnaissance metadynamics method, which employs a self-learning algorithm to construct a bias that pushes the system away from the kinetic traps where it ... [Proc. Natl. Acad. Sci. U.S.A. 109, 5170 (2012)] published Tue Apr 3, 2012.

Formation of embryoid bodies using dielectrophoresis

Sneha Agarwal, Anil Sebastian, Lesley M. Forrester, and Gerard H. Markx
Embryoid body (EB) formation forms an important step in embryonic stem cell differentiation invivo. In murine embryonic stem cell (mESC) cultures EB formation is inhibited by the inclusion of leukaemic inhibitory factor (LIF) in the medium. Assembly of mESCs into aggregates by positive dielectrophor ... [Biomicrofluidics 6, 024101 (2012)] published Tue Apr 3, 2012.

Biopolymer elasticity: Mechanics and thermal fluctuations

Supurna Sinha and Joseph Samuel
We present an analytical study of the role of thermal fluctuations in shaping molecular elastic properties of semiflexible polymers. Our study interpolates between mechanics and statistical mechanics in a controlled way and shows how thermal fluctuations modify the elastic properties of biopolymers. ... [Phys. Rev. E 85, 041802 ] published .

Sheet-like assemblies of spherical particles with point-symmetrical patches

Ethayaraja Mani, Eduardo Sanz, Soumyajit Roy, Marjolein Dijkstra, Jan Groenewold et al.
We report a computational study on the spontaneous self-assembly of spherical particles into two-dimensional crystals. The experimental observation of such structures stabilized by spherical objects appeared paradoxical so far. We implement patchy interactions with the patches point-symmetrically (i ... [J. Chem. Phys. 136, 144706 (2012)] published Wed Apr 11, 2012.

Nucleation of colloids and macromolecules: Does the nucleation pathway matter?

James F. Lutsko
A recent description of diffusion-limited nucleation based on fluctuating hydrodynamics that extends classical nucleation theory predicts a very non-classical two-step scenario whereby nucleation is most likely to occur in spatially extended, low-amplitude density fluctuations. In this paper, it is ... [J. Chem. Phys. 136, 134502 (2012)] published Mon Apr 2, 2012.

Lattice stretching bistability and dynamic heterogeneity

P. L. Christiansen, A. V. Savin, and A. V. Zolotaryuk
A simple one-dimensional lattice model is suggested to describe the experimentally observed plateau in force-stretching diagrams for some macromolecules. This chain model involves the nearest-neighbor interaction of a Morse-like potential (required to have a saturation branch) and a harmonic second- ... [Phys. Rev. E 85, 046601 ] published .

Forced translocation of a polymer: Dynamical scaling versus molecular dynamics simulation

J. L. A. Dubbeldam, V. G. Rostiashvili, A. Milchev, and T. A. Vilgis
We suggest a theoretical description of the force-induced translocation dynamics of a polymer chain through a nanopore. Our consideration is based on the tensile (Pincus) blob picture of a pulled chain and the notion of a propagating front of tensile force along the chain backbone, suggested by Saka ... [Phys. Rev. E 85, 041801 ] published .

Computer simulation of linkage of two ring chains

Zhimin Xiong, Charles C. Han, and Qi Liao
We performed off-lattice Monte Carlo simulations of links of two model ring chains with chain length N up to 32 768 in the theta solution or amorphous bulk state by using a random walk model (Model I), and molecular dynamics simulations of two model ring chains in solution with excluded volume inter ... [J. Chem. Phys. 136, 134902 (2012)] published Wed Apr 4, 2012.

Effective interactions between grafted nanoparticles in a polymer matrix

Dong Meng, Sanat K. Kumar, J. Matthew D. Lane, and Gary S. Grest
Molecular dynamics simulations were used to delineate the separation dependent forces between two polymer-grafted nanoparticles in a polymer melt, the associated potential of mean force (PMF), and the molecular origins of these forces. The nanoparticle radius (=5, in units of the size of the chain m ... [Soft Matter 8, 5002 (2012)] published Thu Apr 12, 2012.

Correlations between mechanical, structural, and dynamical properties of polymer nanocomposites

Aki Kutvonen, Giulia Rossi, and Tapio Ala-Nissila
We study the structural and dynamical mechanisms of reinforcement of a polymer nanocomposite (PNC) via coarse-grained molecular dynamics simulations. In a regime of strong polymer-filler interactions, the stress at failure of the PNC is clearly correlated to structural quantities, such as the filler ... [Phys. Rev. E 85, 041803 ] published .

A highly coarse-grained model to simulate entangled polymer melts

You-Liang Zhu, Hong Liu, and Zhong-Yuan Lu
We introduce a highly coarse-grained model to simulate the entangled polymer melts. In this model, a polymer chain is taken as a single coarse-grained particle, and the creation and annihilation of entanglements are regarded as stochastic events in proper time intervals according to certain rules an ... [J. Chem. Phys. 136, 144903 (2012)] published Fri Apr 13, 2012.

Folding kinetics of a polymer

Stepan RZiCka, David Quigley, and Michael P. Allen
We present the results of computer simulations giving a kinetic insight into the liquid-to-solid transition of a homopolymer chain with short-range interactions. By calculating the absolute rates in each direction of the transition, using molecular dynamics employing the forward flux sampling scheme ... [Phys. Chem. Chem. Phys. 14, 6044 ] published .

High-pressure effect on the dynamics of solvated peptides

Ricky B. Nellas, Mary M. Glover, Donald Hamelberg, and Tongye Shen
The dynamics of peptides has a direct connection to how quickly proteins can alter their conformations. The speed of exploring the free energy landscape depend on many factors, including the physical parameters of the environment, such as pressure and temperature. We performed a series of molecular ... [J. Chem. Phys. 136, 145103 (2012)] published Thu Apr 12, 2012.

MichaelisMenten dynamics of a polymer chain out of a dichotomous ATP-based motor

Alessandro Fiasconaro, Juan Mazo, and Fernando Falo
We present a model of an ATP-fueled molecular machine which pushes a polymer through a pore channel. The machine acts between two levels (workingwaiting), and the working one remains active for a fixed time giving a constant force. The activation rate of the machine can be put in relationship with t ... [New J. Phys. 14, 023004 (2012)] published Tue Apr 3, 2012.

Mechanism of Voltage Gating in Potassium Channels

Morten . Jensen, Vishwanath Jogini, David W. Borhani, Abba E. Leffler, Ron O. Dror et al.
The mechanism of ion channel voltage gatinghow channels open and close in response to voltage changeshas been debated since Hodgkin and Huxley's seminal discovery that the crux of nerve conduction is ion flow across cellular membranes. Using all-atom molecular dynamics simulations, we show how a vol ... [Science 336, 229 (2012)] published Wed Apr 11, 2012.

Effect of channel mutations on the uptake and release of the retinal ligand in opsin

Ronny Piechnick, Eglof Ritter, Peter W. Hildebrand, Oliver P. Ernst, Patrick Scheerer et al.
In the retinal binding pocket of rhodopsin, a Schiff base links the retinal ligand covalently to the Lys296 side chain. Light transforms the inverse agonist 11-cis-retinal into the agonist all-trans-retinal, leading to the active Meta II state. Crystal structures of Meta II and the active conformat ... [Proc. Natl. Acad. Sci. U.S.A. 109, 5247 (2012)] published Tue Apr 3, 2012.

X-Ray propagation imaging of a lipid bilayer in solution

Andre Beerlink, Shashi Thutupalli, Michael Mell, Matthias Bartels, Peter Cloetens et al.
We have used X-ray propagation imaging to visualize a less than 5 nm thick native lipid bilayer membrane freely suspended in aqueous solution. Contrast is formed by free space propagation of hard X-rays, with the membrane illuminated by a nano-focused, partially coherent synchrotron beam, at a contr ... [Soft Matter 8, 4594 (2012)] published Thu Apr 5, 2012.

TWIK1, a unique background channel with variable ion selectivity

Franck C. Chatelain, Delphine Bichet, Dominique Douguet, Sylvain Feliciangeli, Said Bendahhou et al.
TWIK1 belongs to the family of background K channels with two pore domains. In native and transfected cells, TWIK1 is detected mainly in recycling endosomes. In principal cells in the kidney, TWIK1 gene inactivation leads to the loss of a nonselective cationic conductance, an unexpected effect that ... [Proc. Natl. Acad. Sci. U.S.A. 109, 5499 (2012)] published Tue Apr 3, 2012.

High pressure effect on phase transition behavior of lipid bilayers

Kan Lai, Biao Wang, Yong Zhang, and Yongwei Zhang
Phase behavior of lipid bilayers at high pressure is critical to biological processes. Using coarse grained molecular dynamic simulations, we report critical characteristics of dipalmitoylphosphatidylcholine bilayers with applied high pressure, and also show their phase transition by cooling bilayer ... [Phys. Chem. Chem. Phys. 14, 5744 (2012)] published Thu Apr 5, 2012.

Slow growth of the Rayleigh-Plateau instability in aqueous two phase systems

Sam D. Geschiere, Iwona Ziemecka, Volkert van Steijn, Ger J. M. Koper, Jan H. van Esch et al.
This paper studies the Rayleigh-Plateau instability for co-flowing immiscible aqueous polymer solutions in a microfluidic channel. Careful vibration-free experiments with controlled actuation of the flow allowed direct measurement of the growth rate of this instability. Experiments for the well-know ... [Biomicrofluidics 6, 022007 (2012)] published Fri Apr 6, 2012.

Texture defects in lipid membrane domains

Jes Dreier, Jonathan Brewer, and Adam Cohen Simonsen
Important aspects of lateral organization in biomembranes can be addressed in model systems. Recently, it has become clear from polarized fluorescence imaging and X-ray scattering that gel domains in bilayers may contain orientational texture related to the tilted acyl chains. Such internal structur ... [Soft Matter 8, 4894 (2012)] published Thu Apr 12, 2012.

Self-assembled architectures with multiple aqueous compartments

Hans-Peter M. de Hoog, Madhavan Nallani, and Nikodem Tomczak
A vital organizational feature of living cells is that of compartmentalization. This allows cells to run concurrently incompatible metabolic processes and to regulate these processes by selective trans-membrane transport. Although strategies that effectively mimic cell function in simple architectur ... [Soft Matter 8, 4551 (2012)] published Thu Apr 5, 2012.

Structure of components of an intercellular channel complex in sporulating Bacillus subtilis

Vladimir M. Levdikov, Elena V. Blagova, Amanda McFeat, Mark J. Fogg, Keith S. Wilson et al.
Following asymmetric cell division during spore formation in Bacillus subtilis, a forespore expressed membrane protein SpoIIQ, interacts across an intercellular space with a mother cell-expressed membrane protein, SpoIIIAH. Their interaction can serve as a molecular "ratchet" contributing to the mi ... [Proc. Natl. Acad. Sci. U.S.A. 109, 5441 (2012)] published Tue Apr 3, 2012.

Chemical and biological decontamination functions of nanofibrous membranes

Jing Zhu, Qazaleh Bahramian, Philip Gibson, Heidi Schreuder-Gibson, and Gang Sun
Novel composite membranes with poly(vinyl alcohol-co-ethylene-g-diallylmelamine) (PVA-co-PE-g-DAM) nanofibers layered on poly(propylene-g-diallylmelamine) (PP-g-DAM) meltblown nonwoven fabric were successfully developed as lightweight and breathable protective materials with chemical and biological ... [J. Mater. Chem. 22, 8532 ] published .

Nuclear dynamics and spectator effects in resonant inelastic soft x-ray scattering of gas-phase water molecules

Lothar Weinhardt, Andreas Benkert, Frank Meyer, Monika Blum, Regan G. Wilks et al.
The electronic structure of gas-phase HO and DO molecules has been investigated using resonant inelastic soft x-ray scattering (RIXS). We observe spectator shifts for all valence orbitals when exciting into the lowest three absorption resonances. Strong changes of the relative valence orbital emissi ... [J. Chem. Phys. 136, 144311 (2012)] published Thu Apr 12, 2012.

An orbital and electron density analysis of weak interactions in ethanol-water, methanol-water, ethanol and methanol small clusters

Sol M. Mejia, Elizabeth Florez, and Fanor Mondragon
A computational study of (ethanol)-water, n = 1 to 5 heteroclusters was carried out employing the B3LYP/6-31+G(d) approach. The molecular (MO) and atomic (AO) orbital analysis and the topological study of the electron density provided results that were successfully correlated. Results were compared ... [J. Chem. Phys. 136, 144306 (2012)] published Wed Apr 11, 2012.

Auger spectrum of a water molecule after single and double core ionization

L. Inhester, C. F. Burmeister, G. Groenhof, and H. Grubmuller
The high intensity of free electron lasers opens up the possibility to perform single-shot molecule scattering experiments. However, even for small molecules, radiation damage induced by absorption of high intense x-ray radiation is not yet fully understood. One of the striking effects which occurs ... [J. Chem. Phys. 136, 144304 (2012)] published Mon Apr 9, 2012.

Coupled-monomers in molecular assemblies: Theory and application to the water tetramer, pentamer, and ring hexamer

Yimin Wang and Joel M. Bowman
We present extensions to the local-monomer (LMon) Model, a general quantum method to describe coupled intramolecular vibrational modes of a molecular cluster consisting of a set of monomers [Y. Wang and J. M. Bowman, J. Chem. Phys. 134, 154510 (2011)], to incorporate monomer-monomer coupling. A cent ... [J. Chem. Phys. 136, 144113 (2012)] published Thu Apr 12, 2012.

Solvent effect on the folding dynamics and structure of E6-associated protein characterized from ab initio protein folding simulations

Zhijun Xu, Raudah Lazim, Tiedong Sun, Ye Mei, and Dawei Zhang
Solvent effect on protein conformation and folding mechanism of E6-associated protein (E6ap) peptide are investigated using a recently developed charge update scheme termed as adaptive hydrogen bond-specific charge (AHBC). On the basis of the close agreement between the calculated helix contents fro ... [J. Chem. Phys. 136, 135102 (2012)] published Mon Apr 2, 2012.

A phenomenological approach to modeling chemical dynamics in nonlinear and two-dimensional spectroscopy

Krupa Ramasesha, Luigi De Marco, Andrew D. Horning, Aritra Mandal, and Andrei Tokmakoff
We present an approach for calculating nonlinear spectroscopic observables, which overcomes the approximations inherent to current phenomenological models without requiring the computational cost of performing molecular dynamics simulations. The trajectory mapping method uses the semi-classical appr ... [J. Chem. Phys. 136, 134507 (2012)] published Thu Apr 5, 2012.

First-principles calculation of thermodynamic stability of acids and bases under pH environment: A microscopic pH theory

Yong-Hyun Kim, Kwiseon Kim, and S. B. Zhang
Despite being one of the most important thermodynamic variables, pH has yet to be incorporated into first-principles thermodynamics to calculate stability of acidic and basic solutes in aqueous solutions. By treating the solutes as defects in homogeneous liquids, we formulate a first-principles appr ... [J. Chem. Phys. 136, 134112 (2012)] published Fri Apr 6, 2012.

Variational calculation of quantum mechanical/molecular mechanical free energy with electronic polarization of solvent

Hiroshi Nakano and Takeshi Yamamoto
Quantum mechanical/molecular mechanical (QM/MM) free energy calculation presents a significant challenge due to an excessive number of QM calculations. A useful approach for reducing the computational cost is that based on the mean field approximation to the QM subsystem. Here, we describe such a me ... [J. Chem. Phys. 136, 134107 (2012)] published Wed Apr 4, 2012.

A comparison of the value of viscosity for several water models using Poiseuille flow in a nano-channel

A. P. Markesteijn, Remco Hartkamp, S. Luding, and J. Westerweel
The viscosity-temperature relation is determined for the water models SPC/E, TIP4P, TIP4P/Ew, and TIP4P/2005 by considering Poiseuille flow inside a nano-channel using molecular dynamics. The viscosity is determined by fitting the resulting velocity profile (away from the walls) to the continuum sol ... [J. Chem. Phys. 136, 134104 (2012)] published Mon Apr 2, 2012.

A simulation study of the self-assembly of coarse-grained skin lipids

K. R. Hadley and C. McCabe
Computer simulations are an attractive means by which to probe the self-assembly and molecular level organization of lipids in biological membranes. In this work, we study a simple skin lipid system to demonstrate the ability of the coarse-grained models used for fatty acids, cholesterol, and water ... [Soft Matter 8, 4802 ] published .

Response of polymer molecules embedded in a nanodroplet to collisions with a wall

Si Neng Sun and Herbert M. Urbassek
Using molecular-dynamics simulation, we study the collision of polymer-filled water droplets with a wall. We are interested in impact velocities which lead to polymer isolation after the collision. This occurs if the impact energy per solvent molecule, E, exceeds roughly the cohesive energy of the s ... [Soft Matter 8, 4707 (2012)] published Thu Apr 5, 2012.

Internal nonlinear dynamics of a short lattice DNA model in terms of propagating kink-antikink solitons

M. Vanitha and M. Daniel
We study the internal nonlinear dynamics of an inhomogeneous short lattice DNA model by solving numerically the governing discrete perturbed sine-Gordon equations under the limits of a uniform and a nonuniform angular rotation of bases. The internal dynamics is expressed in terms of open-state confi ... [Phys. Rev. E 85, 041911 ] published .

Detailed insight into the hydrogen bonding interactions in acetonemethanol mixtures. A molecular dynamics simulation and Voronoi polyhedra analysis study

Abdenacer Idrissi, Kamil Polok, W. Gadomski, Ivan Vyalov, Alexander Agapov et al.
Voronoi polyhedra (VP) analysis of mixtures of acetone and methanol is reported on the basis of molecular dynamics computer simulations, performed at 300 K and 1 bar. The composition of the systems investigated covers the entire range from neat acetone to neat methanol. Distribution of the volume, r ... [Phys. Chem. Chem. Phys. 14, 5979 ] published .

Energetics of ligand binding to the DNA minor groove

Viktor V. Kostjukov, Adrian A. Hernandez Santiago, Fernando Rojas Rodriguez, Salvador Rosas Castilla, John A. Parkinson et al.
In the present work the decomposition of the total Gibbs free energy of ligand-DNA binding onto various physical terms was accomplished for the group of nine DNA minor groove binders (MGB ligands) differing in both structure and charge state. The decomposition protocol includes the analysis of the m ... [Phys. Chem. Chem. Phys. 14, 5588 (2012)] published Thu Apr 5, 2012.

The importance of the shape of the proteinwater interface of a kinesin motor domain for dynamics of the surface atoms of the protein

Anna Kuffel and Jan Zielkiewicz
A single kinesin motor domain immersed in water has been investigated using molecular dynamics. It has been found that local properties of water in the solvation shell change along with the nature of the neighboring protein surface. However, a detailed analysis leads to the conclusion that the geome ... [Phys. Chem. Chem. Phys. 14, 5561 (2012)] published Thu Apr 5, 2012.

Vibrations and hydrogen bonding in porphycene

Sylwester Gawinkowski, Lukasz Walewski, Alexander Vdovin, Alkwin Slenczka, Stephane Rols et al.
Combined use of IR, Raman, neutron scattering and fluorescence measurements for porphycene isolated in helium nanodroplets, supersonic jet and cryogenic matrices, as well as for solid and liquid solutions, resulted in the assignments of almost all of 108 fundamental vibrations. The puzzling feature ... [Phys. Chem. Chem. Phys. 14, 5489 (2012)] published Thu Apr 5, 2012.

Chemistry in solution: recent techniques and applications using soft X-ray spectroscopy

Kathrin M. Lange, Alexander Kothe, and Emad F. Aziz
The aim of a more precise knowledge about molecular structures and the nature of chemical bonds is the driving force behind the development of numerous experimental methods and theories. Recent soft X-ray based techniques provide novel opportunities for tackling the structure and the dynamics of che ... [Phys. Chem. Chem. Phys. 14, 5331 (2012)] published Thu Apr 5, 2012.

Structural basis of ultraviolet-B perception by UVR8

Di Wu, Qi Hu, Zhen Yan, Wen Chen, Chuangye Yan et al.
The Arabidopsis thaliana protein UVR8 is a photoreceptor for ultraviolet-B. Upon ultraviolet-B irradiation, UVR8 undergoes an immediate switch from homodimer to monomer, which triggers a signalling pathway for ultraviolet protection. The mechanism by which UVR8 senses ultraviolet-B remains largely u ... [Nature 484, 214 (2012)] published Thu Apr 12, 2012.