Virtual Journal of Biological Physics Research

Analytical Results for Size-Topology Correlations in 2D Disk and Cellular Packings

Matthew P. Miklius and Sascha Hilgenfeldt
Random tilings or packings in the plane are characterized by a size distribution of individual elements (domains) and by the statistics of neighbor relations between the domains. Most systems occurring in nature or technology have a unimodal distribution of both areas and number of neighbors. Empiri ... [Phys. Rev. Lett. 108, 015502 ] published .

Nanomechanical actuation driven by light-induced DNA fuel

Kilho Eom, Huihun Jung, Gyudo Lee, Jinsung Park, Kihwan Nam et al.
We report the reversible nanomechanical actuation of a microcantilever driven by the light irradiation-induced conformational changes of i-motif DNA chains, which are functionalized on the cantilever's surface. It is shown that light irradiation-driven nanomechanical actuation can be manipulated usi ... [Chem. Commun. 48, 955 (2012)] published Wed Jan 4, 2012.

Lamination and mixing in laminar flows driven by Lorentz body forces

L. Rossi, D. Doorly, and D. Kustrin
We present a new approach to the design of mixers. This approach relies on a sequence of tailored flows coupled with a new procedure to quantify the local degree of striation, called lamination. Lamination translates to the distance over which the molecular diffusion needs to act to finalise mixing. ... [EPL 97, 14006 (2012)] published Tue Jan 10, 2012.

More effective antimicrobial mastoparan derivatives, generated by 3D-QSAR-Almond and computational mutagenesis

Speranta Avram, Catalin Buiu, Florin Borcan, and Adina-Luminita Milac
Antimicrobial peptides are drugs used against a wide range of pathogens which present a great advantage: in contrast with antibiotics they do not develop resistance. The wide spectrum of antimicrobial peptides advertises them in the research and pharmaceutical industry as attractive starting points ... [Mol. BioSyst. 8, 587 (2012)] published Thu Jan 12, 2012.

Microfluidic wound-healing assay to assess the regenerative effect of HGF on wounded alveolar epithelium

Marcel Felder, Pauline Sallin, Laurent Barbe, Beat Haenni, Amiq Gazdhar et al.
We present a microfluidic epithelial wound-healing assay that allows characterization of the effect of hepatocyte growth factor (HGF) on the regeneration of alveolar epithelium using a flow-focusing technique to create a regular wound in the epithelial monolayer. The phenotype of the epithelial cell ... [Lab Chip 12, 640 (2012)] published Wed Jan 11, 2012.

Label-free real-time imaging in microchip free-flow electrophoresis applying high speed deep UV fluorescence scanning

Stefan Kohler, Stefan Nagl, Stefanie Fritzsche, and Detlev Belder
We report on label-free monitoring of microfluidic free-flow electrophoresis ([mu]FFE) separations in real-time using a custom built high speed deep UV laser scanner. In combination with a novel layout realized in fused silica (FS) FFE chips the setup was successfully applied for continuous separati ... [Lab Chip 12, 458 (2012)] published Wed Jan 11, 2012.

Roughness optimization of electron-beam exposed hydrogen silsesquioxane for immobilization of DNA origami

Faisal A. Shah, Kyoung Nan Kim, Marya Lieberman, and Gary H. Bernstein
A novel way to immobilize deoxyribonucleic acid (DNA) origami on a conventional substrate using hydrogen silsesquioxane (HSQ) as a functionalized platform is demonstrated. An alternative approach to quantifying roughness of the HSQ surfaces for 2D DNA origami immobilization is also introduced. Effec ... [J. Vac. Sci. Technol. B 30, 011806 (2012)] published Thu Jan 12, 2012.

Silver nanosheet-coated inverse opal film as a highly active and uniform SERS substrate

Lifang He, Jianan Huang, Tingting Xu, Limiao Chen, Kui Zhang et al.
The availability of well-controlled and reproducible substrates is critically important for surface-enhanced Raman spectroscopy (SERS)-based applications, but it remains a challenge at present. Herein, we report a facile strategy to prepare a new kind of SERS-active substrate, i.e., a two dimensiona ... [J. Mater. Chem. 22, 1370 (2012)] published Fri Jan 6, 2012.

High-resolution doseresponse screening using droplet-based microfluidics

Oliver J. Miller, Abdeslam El Harrak, Thomas Mangeat, Jean-Christophe Baret, Lucas Frenz et al.
A critical early step in drug discovery is the screening of a chemical library. Typically, promising compounds are identified in a primary screen and then more fully characterized in a doseresponse analysis with 710 data points per compound. Here, we describe a robust microfluidic approach that inc ... [Proc. Natl. Acad. Sci. U.S.A. 109, 378 (2012)] published Tue Jan 10, 2012.

Fabrication of photosensitive multilayered films via layer-by-layer assembly with well controlled porous structure

Cao Li, Kang Wang, Yu-Hui Gong, Ze-Yong Li, Jing Zhang et al.
Photosensitive multilayered films were fabricated via layer-by-layer (LbL) assembly based on 5-(4-aminophenyl)-10,15,20-triphenyl-porphyrin (APP) terminated poly-l-lysine (APP-PLL) and DNA (herring sperm). It was found that the distinctive absorbance of porphyrin at 425 nm after light illumination d ... [J. Mater. Chem. 22, 2045 (2012)] published Wed Jan 11, 2012.

Silica encapsulated SERS nanoprobe conjugated to the bacteriophage tailspike protein for targeted detection of Salmonella

Li-Lin Tay, Ping-Ji Huang, Jamshid Tanha, Shannon Ryan, Xiaohua Wu et al.
Silica-encapsulated Raman-reporter embedded SERS nanoprobes, named nanoaggregate embedded beads (NAEBs), were conjugated to the Salmonella specific tailspike protein (TSP) isolated from the P22 bacteriophage to enable a highly specific and ultrasensitive optical transduction platform. We demonstrate ... [Chem. Commun. 48, 1024 (2012)] published Wed Jan 4, 2012.

Measuring rapid kinetics by a potentiometric method in droplet-based microfluidic devices

Zuoyan Han, Yuen Yan Chang, Shannon Wing Ngor Au, and Bo Zheng
Droplets containing RNA and Mg were generated in microfluidic channels. By integrating a group of pneumatic valves and phase separation channels in the microfluidic system, the rapid RNAMg binding kinetics was studied by measuring the Mg ion concentration using an ion-selective electrode. ... [Chem. Commun. 48, 1601 (2012)] published Thu Jan 12, 2012.

From highly ramified, large scale dendrite patterns of drying alginate/Au NPs solutions to capillary fabrication of lab-scale composite hydrogel microfibers

Samer Darwich, Karine Mougin, and Hamidou Haidara
The processes of complexation, aggregation and self-assembly involving natural polymers are not only ubiquitous in biological systems (proteins), but they are also crucial for environmental and technological applications (humic acids, polysaccharide-based hydrogels). In this paper, we address these ... [Soft Matter 8, 1155 (2012)] published Wed Jan 4, 2012.

Chemiluminescence biosensors for DNA detection using graphene oxide and a horseradish peroxidase-mimicking DNAzyme

Ming Luo, Xi Chen, Guohua Zhou, Xia Xiang, Lu Chen et al.
In this communication, we demonstrate that graphene oxide (GO) greatly inhibits the peroxidatic activity of a horseradish peroxidase-mimicking DNAzyme. Combining this observation with the unique DNA/GO interactions, an ultrasensitive GO-based chemiluminescence DNA biosensing platform is developed. ... [Chem. Commun. 48, 1126 (2012)] published Fri Jan 6, 2012.

A bienzymatic amperometric immunosensor exploiting supramolecular construction for ultrasensitive protein detection

Mayreli Ortiz, Ewelina Maria Wajs, Alex Fragoso, and Ciara K. O'Sullivan
Self-assembly of a ferrocene-appended polymer bearing an antigen fragment and lactate oxidase on a cyclodextrin-modified surface provides a highly sensitive, easy-to-operate and self-sufficient immunosensor. ... [Chem. Commun. 48, 1045 (2012)] published Wed Jan 4, 2012.

Coreshell microgels as smart carriers for enzymes

Nicole Welsch, Alisa L. Becker, Joachim Dzubiella, and Matthias Ballauff
We present a thermodynamic study of the adsorption of lysozyme on a negatively charged coreshell microgel at pH 7.2. The carrier particles consist of a polystyrene core onto which a charged poly(N-isopropylacrylamide-co-acrylic acid) network is attached. Isothermal titration calorimetry (ITC) is use ... [Soft Matter 8, 1428 (2012)] published Thu Jan 12, 2012.

Spintronic platforms for biomedical applications

P. P. Freitas, F. A. Cardoso, V. C. Martins, S. A. M. Martins, J. Loureiro et al.
Since the fundamental discovery of the giant magnetoresistance many spintronic devices have been developed and implemented in our daily life (e.g. information storage and automotive industry). Lately, advances in the sensors technology (higher sensitivity, smaller size) have potentiated other applic ... [Lab Chip 12, 546 (2012)] published Wed Jan 11, 2012.

Compatible immuno-NASBA LOC device for quantitative detection of waterborne pathogens: design and validation

Xinyan Zhao, Tao Dong, Zhaochu Yang, Nuno Pires, and Nils Hoivik
Waterborne pathogens usually pose a global threat to animals and human beings. There has been a growing demand for convenient and sensitive tools to detect the potential emerging pathogens in water. In this study, a lab-on-a-chip (LOC) device based on the real-time immuno-NASBA (immuno-nucleic acid ... [Lab Chip 12, 602 (2012)] published Wed Jan 11, 2012.

Forster resonance energy transfer imaging in vivo with approximated radiative transfer equation

Vadim Y. Soloviev, James McGinty, Daniel W. Stuckey, Romain Laine, Marzena Wylezinska-Arridge et al.
We describe a new light transport model, which was applied to three-dimensional lifetime imaging of Forster resonance energy transfer in mice in vivo. The model is an approximation to the radiative transfer equation and combines light diffusion and ray optics. This approximation is well adopted to w ... [Appl. Opt. 50, 6583 (2012)] published Tue Jan 3, 2012.

Synthesis and functionalization of poly(ethylene glycol) microparticles as soft colloidal probes for adhesion energy measurements

Daniel Pussak, Muriel Behra, Stephan Schmidt, and Laura Hartmann
We report on the synthesis and operation of new soft colloidal probes (SCPs) as sensors for adhesion energy measurements. The measurements involve determination of the thermodynamic work of adhesion using the JohnsonKendallRoberts (JKR) approach. To maximize the sensitivity as well as the specificit ... [Soft Matter 8, 1664 (2012)] published Thu Jan 12, 2012.

Note: An adhesion measurement setup for bioinspired fibrillar surfaces using flat probes

E. Kroner, J. Blau, and E. Arzt
Current adhesion measurement setups designed for experiments on bioinspired fibrillar surfaces, either commercial or constructed in-house, do not allow adhesion measurements with in situ visualization, high resolution, high force range, and controlled alignment at the same time. In this paper a new ... [Rev. Sci. Instrum. 83, 016101 (2012)] published Mon Jan 9, 2012.

A new borehole wire extensometer with high accuracy and stability for observation of local geodynamic processes

Gy. Mentes
Very stable and reliable instruments with high accuracy are required in field measurements for continuous monitoring local geodynamic processes, such as tectonic movements, ground motions in landslide prone areas, etc. A sensitive borehole wire extensometer with low energy consumption was developed ... [Rev. Sci. Instrum. 83, 015109 (2012)] published Fri Jan 13, 2012.

Fast on-wafer electrical, mechanical, and electromechanical characterization of piezoresistive cantilever force sensors

G. Tosolini, L. G. Villanueva, F. Perez-Murano, and J. Bausells
Validation of a technological process requires an intensive characterization of the performance of the resulting devices, circuits, or systems. The technology for the fabrication of micro and nanoelectromechanical systems (MEMS and NEMS) is evolving rapidly, with new kind of device concepts for appl ... [Rev. Sci. Instrum. 83, 015002 (2012)] published Wed Jan 11, 2012.

Magnetic nanomanipulations inside living cells compared with passive tracking of nanoprobes to get consensus for intracellular mechanics

Damien Robert, Kelly Aubertin, Jean-Claude Bacri, and Claire Wilhelm
During the last decade, the development of nanomaterials to penetrate inside living cells has been the focus of a large number of studies, with applications for the biomedical field. However, the further dynamics of these nanomaterials inside the cells is dictated by the intracellular environment an ... [Phys. Rev. E 85, 011905 ] published .

Highly-integrated lab-on-chip system for point-of-care multiparameter analysis

Soeren Schumacher, Jorg Nestler, Thomas Otto, Michael Wegener, Eva Ehrentreich-Forster et al.
A novel innovative approach towards a marketable lab-on-chip system for point-of-care in vitro diagnostics is reported. In a consortium of seven Fraunhofer Institutes a lab-on-chip system called Fraunhofer ivD-platform has been established which opens up the possibility for an on-site analysis at lo ... [Lab Chip 12, 464 (2012)] published Wed Jan 11, 2012.

Partially coherent lensfree tomographic microscopy [Invited]

Serhan O. Isikman, Waheb Bishara, and Aydogan Ozcan
Optical sectioning of biological specimens provides detailed volumetric information regarding their internal structure. To provide a complementary approach to existing three-dimensional (3D) microscopy modalities, we have recently demonstrated lensfree optical tomography that offers high-throughput ... [Appl. Opt. 50, H253 (2012)] published Tue Jan 3, 2012.

Optically Trapped Gold Nanoparticle Enables Listening at the Microscale

Alexander Ohlinger, Andras Deak, Andrey A. Lutich, and Jochen Feldmann
We explore a new application of optical tweezers for ultrasensitive detection of sound waves in liquid media. Position tracking of a single gold nanoparticle confined in a three-dimensional optical trap is used to readout acoustic vibrations at a sound power level down to -60 dB, causing a ~90 [mu ... [Phys. Rev. Lett. 108, 018101 ] published .

Acoustical properties of wood in string instruments soundboards and tuned idiophones: Biological and cultural diversity

Iris Bremaud
The acoustical properties of wood for instruments have mostly been studied on a few archetypal woods in Western musical instruments. The objective of this paper is to extend knowledge on the diversity in wood properties and uses in instruments from different geo-cultural areas. A wide set of data ha ... [J. Acoust. Soc. Am. 131, 807 (2012)] published Fri Jan 13, 2012.

Do trumpet players tune resonances of the vocal tract?

Jer-Ming Chen, John Smith, and Joe Wolfe
The acoustic impedance spectrum was measured in the mouths of seven trumpeters while they played normal notes and while they practiced bending the pitch below or above the normal value. The peaks in vocal tract impedance usually had magnitudes rather smaller than those of the bore of the trumpet. Ov ... [J. Acoust. Soc. Am. 131, 722 (2012)] published Fri Jan 13, 2012.

Some basic relations for ultrasonic fields from circular transducers with a central hole

K. Beissner
Ultrasonic transducers with a central hole are increasingly in use in high-intensity therapeutic ultrasound and similar medical applications. The hole is intended for the addition of a diagnostic device. Some fundamental properties of the fields produced by such transducers are investigated here the ... [J. Acoust. Soc. Am. 131, 620 (2012)] published Fri Jan 13, 2012.

Human elbow joint angle estimation using electromyogram signal processing

H.-J. Yu, A.Y. Lee, and Y. Choi
This study proposes a real-time joint angle estimation method of human elbow by processing a biomedical signal of surface synergistic EMG (electromyogram) measured between biceps brachii and triceps brachii simultaneously. Actually, the EMG is known as a non-stationary signal, but the authors assume ... [IET Signal Process. 5, 767 (2012)] published Wed Jan 4, 2012.

Resistive pulse sensing of magnetic beads and supraparticle structures using tunable pores

Geoff R. Willmott, Mark Platt, and Gil U. Lee
Tunable pores (TPs) have been used for resistive pulse sensing of 1 [mu]m superparamagnetic beads, both dispersed and within a magnetic field. Upon application of this field, magnetic supraparticle structures (SPSs) were observed. Onset of aggregation was most effectively indicated by an increase in ... [Biomicrofluidics 6, 014103 (2012)] published Thu Jan 12, 2012.

Electrotaxis of lung cancer cells in ordered three-dimensional scaffolds

Yung-Shin Sun, Shih-Wei Peng, Keng-Hui Lin, and Ji-Yen Cheng
In this paper, we report a new method to incorporate 3D scaffold with electrotaxis measurement in the microfluidic device. The electrotactic response of lung cancer cells in the 3D foam scaffolds which resemble the in vivo pulmonary alveoli may give more insight on cellular behaviors in vivo. The 3D ... [Biomicrofluidics 6, 014102 (2012)] published Wed Jan 4, 2012.

Optical-resolution photoacoustic microscopy based on two-dimensional scanning galvanometer

Yi Yuan, Sihua Yang, and Da Xing
An optical-resolution photoacoustic microscopy system was designed and fabricated by integration of a two-dimensional scanning galvanometer, an objective lens, an unfocused ultrasound transducer, and a sample stage. The lateral resolution of the system was measured to be ~500 nm. Ex vivo erythrocyte ... [Appl. Phys. Lett. 100, 023702 (2012)] published Mon Jan 9, 2012.

A physical approach to the automated classification of clinical percussion sounds

M. A. Pantea, R. Gr. Maev, E. V. Malyarenko, and A. E. Baylor
Chest percussion is a traditional technique used for the physical examination of pulmonary injuries and diseases. It is a method of tapping body parts with fingers or small instruments to evaluate the size, consistency, borders, and presence of fluid/air in the lungs and abdomen. Percussion has been ... [J. Acoust. Soc. Am. 131, 608 (2012)] published Fri Jan 13, 2012.

Quantification of glistenings in intraocular lenses using a ballistic-photon removing integrating-sphere method

Do-Hyun Kim, Robert H. James, Robert J. Landry, Don Calogero, James Anderson et al.
An alternative method for quantification of glistenings in intraocular lenses (IOLs) using an integrating sphere with an adjustable back aperture to remove ballistic photons is presented. Glistenings in soft IOLs have been known for more than a decade; however, their severity and visual impact are s ... [Appl. Opt. 50, 6461 (2012)] published Tue Jan 3, 2012.

Double-functionalized nanopore-embedded gold electrodes for rapid DNA sequencing

Biswarup Pathak, Henrik Lofas, Jariyanee Prasongkit, Anton Grigoriev, Rajeev Ahuja et al.
We have studied the effect of double-functionalization on gold electrodes for improving nanopore-based DNA sequencing. The functionalizing molecular probes are, respectively, capable of temporarily forming hydrogen bonds with both the nucleobase part and the phosphate group of the target DNA, thus p ... [Appl. Phys. Lett. 100, 023701 (2012)] published Mon Jan 9, 2012.

Microfluidic carbon-blackened polydimethylsiloxane device with reduced ultra violet background fluorescence for simultaneous two-color ultra violet/visible-laser induced fluorescence detection in single cell analysis

Lukas Galla, Dominik Greif, Jan Regtmeier, and Dario Anselmetti
In single cell analysis (SCA), individual cell-specific properties and inhomogeneous cellular responses are being investigated that is not subjected to ensemble-averaging or heterogeneous cell population effects. For proteomic single cell analysis, ultra-sensitive and reproducible separation and det ... [Biomicrofluidics 6, 014104 (2012)] published Thu Jan 12, 2012.

A nanoporous optofluidic microsystem for highly sensitive and repeatable surface enhanced Raman spectroscopy detection

Soroush H. Yazdi and Ian M. White
We report the demonstration of an optofluidic surface enhanced Raman spectroscopy (SERS) device that leverages a nanoporous microfluidic matrix to improve the SERS detection performance by more than two orders of magnitude as compared to a typical open microfluidic channel. Although it is a growing ... [Biomicrofluidics 6, 014105 (2012)] published Fri Jan 13, 2012.

Biomolecule detection based on Si single-electron transistors for highly sensitive integrated sensors on a single chip

Takashi Kudo and Anri Nakajima
Biomolecule detection was achieved using a Si single-electron transistor (SET) for highly-sensitive detection. A multiple-island channel-structure was used for the SET to enable room-temperature operation and to increase sensitivity. Coulomb oscillation shifted against the gate voltage due to biotin ... [Appl. Phys. Lett. 100, 023704 (2012)] published Thu Jan 12, 2012.

Label-free detection of DNA using high-kappa LuTiO electrolyte-insulator-semiconductors

Tung-Ming Pan, Kung-Yuan Chang, Chao-Wen Lin, Shiao-Wen Tsai, and Min-Hsien Wu
In this study, we propose a disposable poly-N-isopropylacrylamide (PNIPAAm) as an immobilizing biological material based electrolyte-insulator-semiconductor (EIS) device for DNA detection, prepared from a high-kappa LuTiO sensing membrane. X-ray diffraction, X-ray photoelectron spectroscopy, and ato ... [J. Mater. Chem. 22, 1358 (2012)] published Fri Jan 6, 2012.

Surfactant ion-selective electrodes: A promising approach to the study of the aggregation of ionic surfactants in solution

Guobao Li, Hongmin Ma, and Jingcheng Hao
The potentiometric method based on surfactant ion-selective electrodes (SISEs) was broadly applied to ionic surfactants in solution due to the change in their activities, i.e., concentration in dilute solution, of both the counterions and ionic surfactants at the point of aggregation. The monomeric ... [Soft Matter 8, 896 (2012)] published Wed Jan 4, 2012.

Exploring low-positively charged thermosensitive copolymers as gene delivery vectors

Zheyu Shen, Bingyang Shi, Hu Zhang, Jingxiu Bi, and Sheng Dai
One of the largest challenges in gene therapy is to develop an efficient delivery vector without cytotoxicity. In this study, we propose a new concept in exploring low-positively charged thermosensitive copolymers as gene delivery vectors. Two types of copolymers, random copolymers (RCs) and blocky ... [Soft Matter 8, 1385 (2012)] published Thu Jan 12, 2012.

Exonuclease-assisted cascaded recycling amplification for label-free detection of DNA

Sai Bi, Li Li, and Yangyang Cui
The network consisting of three kinds of unlabeled stem-loop DNA molecular beacons (MBs) is activated by target DNA in the presence of exonuclease-III (Exo-III), achieving the concept of exonuclease-assisted cascaded recycling amplification (Exo-CRA) for DNA detection with a wide dynamic range of 8 ... [Chem. Commun. 48, 1018 (2012)] published Wed Jan 4, 2012.

The effect of protein shells on the antioxidant activity of protein-encapsulated platinum nanoparticles

Boi Hoa San, Sang Hyun Moh, and Kyeong Kyu Kim
Protein shells have been used as nano-platforms for the synthesis of metallic nanoparticles for their biomedical and biocatalytic applications. However, it is challenging to maximize the catalytic activity of nanoparticles encapsulated by protein shells, as little research exists regarding their eff ... [J. Mater. Chem. 22, 1774 (2012)] published Wed Jan 11, 2012.

Engineered (hep/pARG) polyelectrolyte capsules for sustained release of bioactive TGF-beta1

Liesbeth J. De Cock, Olivier De Wever, Sandra Van Vlierberghe, Els Vanderleyden, Peter Dubruel et al.
Spatial and temporal controlled delivery of growth factors which contribute to efficient repair upon tissue injury or failure remains a major challenge in tissue engineering. In this paper, we evaluated polyelectrolyte multilayer microcapsules to control spatiotemporal release of transforming growth ... [Soft Matter 8, 1146 (2012)] published Wed Jan 4, 2012.

Controlled hydrogel photopolymerization inside live systems by X-ray irradiation

S.-Ja Tseng, Chia-Chi Chien, Zi-Xian Liao, Hsiang-Hisn Chen, Yi-Da Kang et al.
We successfully demonstrate the in situ formation by X-ray irradiation induced polymerization of a three-dimensional (3D) hydrogel based on poly(ethylene glycol) (PEG) diacrylate (PEG DA), with the option of heparin incorporation to enhance cell adhesion. The polymerization reaction can be completed ... [Soft Matter 8, 1420 (2012)] published Thu Jan 12, 2012.

Magnetoacoustic imaging of magnetic iron oxide nanoparticles embedded in biological tissues with microsecond magnetic stimulation

Gang Hu and Bin He
We present an experimental study on magnetoacoustic imaging of superparamagnetic iron oxide (SPIO) nanoparticles embedded in biological tissues. In experiments, a large-current-carrying coil is used to deliver microsecond pulsed magnetic stimulation to samples. The ultrasound signals induced by magn ... [Appl. Phys. Lett. 100, 013704 (2012)] published Fri Jan 6, 2012.

Incorporating microorganisms into polymer layers provides bioinspired functional living materials

Lukas C. Gerber, Fabian M. Koehler, Robert N. Grass, and Wendelin J. Stark
Artificial two-dimensional biological habitats were prepared from porous polymer layers and inoculated with the fungus Penicillium roqueforti to provide a living material. Such composites of classical industrial ingredients and living microorganisms can provide a novel form of functional or smart m ... [Proc. Natl. Acad. Sci. U.S.A. 109, 90 (2012)] published Fri Jan 6, 2012.

Efficient optical trapping using small arrays of plasmonic nanoblock pairs

Yoshito Tanaka and Keiji Sasaki
We report that a small two-dimensional array of gold nanoblock pairs separated by a nanometric gap significantly improves the performance of optical trapping compared to a single nanoblock pair. The array of 4 x 4 pairs suppresses the Brownian motion of a trapped 1 [mu]m diameter particle by a fac ... [Appl. Phys. Lett. 100, 021102 (2012)] published Mon Jan 9, 2012.

Synaptic Bistability Due to Nucleation and Evaporation of Receptor Clusters

V. M. Burlakov, N. Emptage, A. Goriely, and P. C. Bressloff
We introduce a bistability mechanism for long-term synaptic plasticity based on switching between two metastable states that contain significantly different numbers of synaptic receptors. One state is characterized by a two-dimensional gas of mobile interacting receptors and is stabilized against cl ... [Phys. Rev. Lett. 108, 028101 ] published .

Optimized reduction of uncertainty in bursty human dynamics

Hang-Hyun Jo, Eunyoung Moon, and Kimmo Kaski
Human dynamics is known to be inhomogeneous and bursty but the detailed understanding of the role of human factors in bursty dynamics is still lacking. In order to investigate their role we devise an agent-based model, where an agent in an uncertain situation tries to reduce the uncertainty by commu ... [Phys. Rev. E 85, 016102 ] published .

Optimal Intermittence in Search Strategies under Speed-Selective Target Detection

Daniel Campos, Vicenc Mendez, and Frederic Bartumeus
Random search theory has been previously explored for both continuous and intermittent scanning modes with full target detection capacity. Here we present a new class of random search problems in which a single searcher performs flights of random velocities, the detection probability when it passes ... [Phys. Rev. Lett. 108, 028102 ] published .

Exploring the dynamics of dimer crossing over a Kramers type potential

Mesfin Asfaw and Yohannes Shiferaw
We explore the escape rate of a dimer crossing a potential barrier using both analytical and numerical approaches. We find that for small coupling strength k, the barrier hopping can be well approximated by a two step reaction scheme where one monomer hops over the barrier and is then followed by th ... [J. Chem. Phys. 136, 025101 (2012)] published Tue Jan 10, 2012.

Brownian needle in dire straits: Stochastic motion of a rod in very confined narrow domains

D. Holcman and Z. Schuss
We study the mean turnaround time of a Brownian needle in a narrow planar strip. When the needle is only slightly shorter than the width of the strip, the computation becomes a nonstandard narrow escape problem. We develop a boundary layer method, based on a conformal mapping of cusplike narrow stra ... [Phys. Rev. E 85, 010103 ] published .

Optimality and thermodynamics determine the evolution of transcriptional regulatory networks

Marco Avila-Elchiver, Deepak Nagrath, and Martin L. Yarmush
Transcriptional motifs are small regulatory interaction patterns that regulate biological functions in highly-interacting cellular networks. Recently, attempts have been made to explain the significance of transcriptional motifs through dynamic function. However, fundamental questions remain unanswe ... [Mol. BioSyst. 8, 511 (2012)] published Thu Jan 12, 2012.

Cultural diversification promotes rapid phenotypic evolution in Xavante Indians

Tabita Hunemeier, Jorge Gomez-Valdes, Monica Ballesteros-Romero, Soledad de Azevedo, Neus Martinez-Abadias et al.
Shifts in social structure and cultural practices can potentially promote unusual combinations of allele frequencies that drive the evolution of genetic and phenotypic novelties during human evolution. These cultural practices act in combination with geographical and linguistic barriers and can pro ... [Proc. Natl. Acad. Sci. U.S.A. 109, 73 (2012)] published Fri Jan 6, 2012.

Plant Species Richness and Ecosystem Multifunctionality in Global Drylands

Fernando T. Maestre, Jos L. Quero, Nicholas J. Gotelli, Adrin Escudero, Victoria Ochoa et al.
Experiments suggest that biodiversity enhances the ability of ecosystems to maintain multiple functions, such as carbon storage, productivity, and the buildup of nutrient pools (multifunctionality). However, the relationship between biodiversity and multifunctionality has never been assessed globall ... [Science 335, 214 ] published .

Supercooperation in evolutionary games on correlated weighted networks

Pierre Buesser and Marco Tomassini
In this work we study the behavior of classical two-person, two-strategies evolutionary games on a class of weighted networks derived from Barabasi-Albert and random scale-free unweighted graphs. Using customary imitative dynamics, our numerical simulation results show that the presence of link weig ... [Phys. Rev. E 85, 016107 ] published .

Fitness Trade-Offs and Environmentally Induced Mutation Buffering in Isogenic C. elegans

M. Olivia Casanueva, Alejandro Burga, and Ben Lehner
Mutations often have consequences that vary across individuals. Here, we show that the stimulation of a stress response can reduce mutation penetrance in Caenorhabditis elegans. Moreover, this induced mutation buffering varies across isogenic individuals because of interindividual differences in str ... [Science 335, 82 (2012)] published Fri Jan 6, 2012.

Langerhans Cells Facilitate Epithelial DNA Damage and Squamous Cell Carcinoma

Badri G. Modi, Jason Neustadter, Elisa Binda, Julia Lewis, Renata B. Filler et al.
Polyaromatic hydrocarbons (PAHs) are prevalent, potent carcinogens, and 7,12-dimethylbenz[a]anthracene (DMBA) is a model PAH widely used to study tumorigenesis. Mice lacking Langerhans cells (LCs), a signatory epidermal dendritic cell (DC), are protected from cutaneous chemical carcinogenesis, indep ... [Science 335, 104 (2012)] published Fri Jan 6, 2012.

Wip1 promotes RUNX2-dependent apoptosis in p53-negative tumors and protects normal tissues during treatment with anticancer agents

Anastasia R. Goloudina, Kan Tanoue, Arlette Hammann, Eric Fourmaux, Xavier Le Guezennec et al.
The inactivation of the p53 tumor suppressor pathway in many cancers often increases their resistance to anticancer therapy. Here we show that a previously proposed strategy directed to Wip1 inhibition could be ineffective in tumors lacking p53. On the contrary, Wip1 overexpression sensitized these ... [Proc. Natl. Acad. Sci. U.S.A. 109, E68 (2012)] published Tue Jan 10, 2012.

Targeting protein-trafficking pathways alters melanoma treatment sensitivity

Zhi-ming Huang, Milka Chinen, Philip J. Chang, Tong Xie, Lily Zhong et al.
Protein-trafficking pathways are targeted here in human melanoma cells using methods independent of oncogene mutational status, and the ability to up-regulate and down-regulate tumor treatment sensitivity is demonstrated. Sensitivity of melanoma cells to cis-diaminedichloroplatinum II (cDDP, cis-pl ... [Proc. Natl. Acad. Sci. U.S.A. 109, 553 (2012)] published Tue Jan 10, 2012.

Genome architectures revealed by tethered chromosome conformation capture and population-based modeling

Reza Kalhor, Harianto Tjong, Nimanthi Jayathilaka, Frank Alber, and Lin Chen
We describe tethered conformation capture (TCC), a method for genome-wide mapping of chromatin interactions. By performing ligations on solid substrates rather than in solution, TCC substantially enhances the signal-to-noise ratio, thereby facilitating a detailed analysis of interactions within and ... [Nature Biotechnol. 30, 90 (2012)] published Tue Jan 10, 2012.

Label-free multiphoton imaging and photoablation of preinvasive cancer cells

Shuangmu Zhuo, Jianxin Chen, Guizhu Wu, Xiaoqin Zhu, Xingshan Jiang et al.
Detection and treatment of early lesions in epithelial tissue offer several possibilities for curing cancer, but it is challenging. Here, we present an optical technique, the combination of multiphoton imaging and absorption, to label-freely detect and ablate preinvasive cancer cells in epithelial t ... [Appl. Phys. Lett. 100, 023703 (2012)] published Tue Jan 10, 2012.

Analyzing the metabolic stress response of recombinant Escherichia coli cultures expressing human interferon-beta in high cell density fed batch cultures using time course transcriptomic data

Anuradha B. Singh, Ashish K. Sharma, and Krishna J. Mukherjee
Fed batch cultures expressing recombinant interferon beta under the T7 promoter were run with different exponential feeding rates of a complex substrate and induced at varying cell densities. Post-induction profiles of the specific product formation rates showed a strong dependence on the specific g ... [Mol. BioSyst. 8, 615 (2012)] published Thu Jan 12, 2012.

An impaired mitochondrial electron transport chain increases retention of the hypoxia imaging agent diacetylbis(4-methylthiosemicarbazonato)copper

Paul S. Donnelly, Jeffrey R. Liddell, SinChun Lim, Brett M. Paterson, Michael A. Cater et al.
Radiolabeled diacetylbis(4-methylthiosemicarbazonato)copper [Cu(atsm)] is an effective positron-emission tomography imaging agent for myocardial ischemia, hypoxic tumors, and brain disorders with regionalized oxidative stress, such as mitochondrial myopathy, encephalopathy, and lactic acidosis with ... [Proc. Natl. Acad. Sci. U.S.A. 109, 47 (2012)] published Fri Jan 6, 2012.

Statistical mechanics model of angiogenic tumor growth

Antonio Luis Ferreira, Dorota Lipowska, and Adam Lipowski
We examine a lattice model of tumor growth where the survival of tumor cells depends on the supplied nutrients. When such a supply is random, the extinction of tumors belongs to the directed percolation universality class. However, when the supply is correlated with the distribution of tumor cells, ... [Phys. Rev. E 85, 010901 ] published .

A microRNA regulon that mediates endothelial recruitment and metastasis by cancer cells

Kim J. Png, Nils Halberg, Mitsukuni Yoshida, and Sohail F. Tavazoie
Metastatic progression of cancer is a complex and clinically daunting process. We previously identified a set of human microRNAs (miRNAs) that robustly suppress breast cancer metastasis to lung and bone and which display expression levels that predict human metastasis. Although these findings revea ... [Nature 481, 190 (2012)] published Thu Jan 12, 2012.

Single-cell proteomic chip for profiling intracellular signaling pathways in single tumor cells

Qihui Shi, Lidong Qin, Wei Wei, Feng Geng, Rong Fan et al.
We describe a microchip designed to quantify the levels of a dozen cytoplasmic and membrane proteins from single cells. We use the platform to assess proteinprotein interactions associated with the EGF-receptor-mediated PI3K signaling pathway. Single-cell sensitivity is achieved by isolating a defi ... [Proc. Natl. Acad. Sci. U.S.A. 109, 419 (2012)] published Tue Jan 10, 2012.

The genetic basis of early T-cell precursor acute lymphoblastic leukaemia

Jinghui Zhang, Li Ding, Linda Holmfeldt, Gang Wu, Sue L. Heatley et al.
Early T-cell precursor acute lymphoblastic leukaemia (ETP ALL) is an aggressive malignancy of unknown genetic basis. We performed whole-genome sequencing of 12 ETP ALL cases and assessed the frequency of the identified somatic mutations in 94 T-cell acute lymphoblastic leukaemia cases. ETP ALL was c ... [Nature 481, 157 (2012)] published Thu Jan 12, 2012.

Targeted RNA sequencing reveals the deep complexity of the human transcriptome

Tim R Mercer, Daniel J Gerhardt, Marcel E Dinger, Joanna Crawford, Cole Trapnell et al.
Transcriptomic analyses have revealed an unexpected complexity to the human transcriptome, whose breadth and depth exceeds current RNA sequencing capability. Using tiling arrays to target and sequence select portions of the transcriptome, we identify and characterize unannotated transcripts whose r ... [Nature Biotechnol. 30, 99 (2012)] published Tue Jan 10, 2012.

Performance comparison of whole-genome sequencing platforms

Hugo Y K Lam, Michael J Clark, Rui Chen, Rong Chen, Georges Natsoulis et al.
Whole-genome sequencing is becoming commonplace, but the accuracy and completeness of variant calling by the most widely used platforms from Illumina and Complete Genomics have not been reported. Here we sequenced the genome of an individual with both technologies to a high average coverage of 76, a ... [Nature Biotechnol. 30, 78 (2012)] published Tue Jan 10, 2012.

Extensive genetic diversity and substructuring among zebrafish strains revealed through copy number variant analysis

Kim H. Brown, Kimberly P. Dobrinski, Arthur S. Lee, Omer Gokcumen, Ryan E. Mills et al.
Copy number variants (CNVs) represent a substantial source of genomic variation in vertebrates and have been associated with numerous human diseases. Despite this, the extent of CNVs in the zebrafish, an important model for human disease, remains unknown. Using 80 zebrafish genomes, representing th ... [Proc. Natl. Acad. Sci. U.S.A. 109, 529 (2012)] published Tue Jan 10, 2012.

A sensing array of radically coupled genetic biopixels

Arthur Prindle, Phillip Samayoa, Ivan Razinkov, Tal Danino, Lev S. Tsimring et al.
Although there has been considerable progress in the development of engineering principles for synthetic biology, a substantial challenge is the construction of robust circuits in a noisy cellular environment. Such an environment leads to considerable intercellular variability in circuit behaviour, ... [Nature 481, 39 (2012)] published Fri Jan 6, 2012.

Draft genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor farmers

Rajeev K Varshney, Wenbin Chen, Yupeng Li, Arvind K Bharti, Rachit K Saxena et al.
Pigeonpea is an important legume food crop grown primarily by smallholder farmers in many semi-arid tropical regions of the world. We used the Illumina next-generation sequencing platform to generate 237.2 Gb of sequence, which along with Sanger-based bacterial artificial chromosome end sequences an ... [Nature Biotechnol. 30, 83 (2012)] published Tue Jan 10, 2012.

Optimized filtering reduces the error rate in detecting genomic variants by short-read sequencing

Joke Reumers, Peter De Rijk, Hui Zhao, Anthony Liekens, Dominiek Smeets et al.
Distinguishing single-nucleotide variants (SNVs) from errors in whole-genome sequences remains challenging. Here we describe a set of filters, together with a freely accessible software tool, that selectively reduce error rates and thereby facilitate variant detection in data from two short-read seq ... [Nature Biotechnol. 30, 61 (2012)] published Tue Jan 10, 2012.

Building stem-cell genomics in California and beyond

Natalie D DeWitt, Michael P Yaffe, and Alan Trounson
Abstract not available. [Nature Biotechnol. 30, 20 (2012)] published Tue Jan 10, 2012.

Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes

Xun Xu, Xin Liu, Song Ge, Jeffrey D Jensen, Fengyi Hu et al.
Rice is a staple crop that has undergone substantial phenotypic and physiological changes during domestication. Here we resequenced the genomes of 40 cultivated accessions selected from the major groups of rice and 10 accessions of their wild progenitors (Oryza rufipogon and Oryza nivara) to >15 ra ... [Nature Biotechnol. 30, 105 (2012)] published Tue Jan 10, 2012.

Gene order and chromosome dynamics coordinate spatiotemporal gene expression during the bacterial growth cycle

Patrick Sobetzko, Andrew Travers, and Georgi Muskhelishvili
In Escherichia coli crosstalk between DNA supercoiling, nucleoid-associated proteins and major RNA polymerase sigma initiation factors regulates growth phase-dependent gene transcription. We show that the highly conserved spatial ordering of relevant genes along the chromosomal replichores largely ... [Proc. Natl. Acad. Sci. U.S.A. 109, E42 (2012)] published Tue Jan 10, 2012.

Using pathway modules as targets for assay development in xenobiotic screening

Richard S. Judson, Holly M. Mortensen, Imran Shah, Thomas B. Knudsen, and Fathi Elloumi
Toxicology and pharmaceutical research is increasingly making use of high throughout-screening (HTS) methods to assess the effects of chemicals on molecular pathways, cells and tissues. Whole-genome microarray analysis provides broad information on the response of biological systems to chemical expo ... [Mol. BioSyst. 8, 531 (2012)] published Thu Jan 12, 2012.

Stochastic simulation of chemically reacting systems using multi-core processors

Colin S. Gillespie
In recent years, computer simulations have become increasingly useful when trying to understand the complex dynamics of biochemical networks, particularly in stochastic systems. In such situations stochastic simulation is vital in gaining an understanding of the inherent stochasticity present, as th ... [J. Chem. Phys. 136, 014101 (2012)] published Tue Jan 3, 2012.

Metagenomic systems biology of the human gut microbiome reveals topological shifts associated with obesity and inflammatory bowel disease

Sharon Greenblum, Peter J. Turnbaugh, and Elhanan Borenstein
The human microbiome plays a key role in a wide range of host-related processes and has a profound effect on human health. Comparative analyses of the human microbiome have revealed substantial variation in species and gene composition associated with a variety of disease states but may fall short ... [Proc. Natl. Acad. Sci. U.S.A. 109, 594 (2012)] published Tue Jan 10, 2012.

Reconstruction of Arabidopsis metabolic network models accounting for subcellular compartmentalization and tissue-specificity

Shira Mintz-Oron, Sagit Meir, Sergey Malitsky, Eytan Ruppin, Asaph Aharoni et al.
Plant metabolic engineering is commonly used in the production of functional foods and quality trait improvement. However, to date, computational model-based approaches have only been scarcely used in this important endeavor, in marked contrast to their prominent success in microbial metabolic engi ... [Proc. Natl. Acad. Sci. U.S.A. 109, 339 (2012)] published Fri Jan 6, 2012.

Competition for Catalytic Resources Alters Biological Network Dynamics

Yannick Rondelez
Genetic regulation networks orchestrate many complex cellular behaviors. Dynamic operations that take place within cells are thus dependent on the gene expression machinery, enabled by powerful enzymes such as polymerases, ribosomes, or nucleases. These generalist enzymes typically process many diff ... [Phys. Rev. Lett. 108, 018102 ] published .

The reconstruction and analysis of tissue specific human metabolic networks

Tong Hao, Hong-Wu Ma, Xue-Ming Zhao, and Igor Goryanin
Human tissues have distinct biological functions. Many proteins/enzymes are known to be expressed only in specific tissues and therefore the metabolic networks in various tissues are different. Though high quality global human metabolic networks and metabolic networks for certain tissues such as liv ... [Mol. BioSyst. 8, 663 (2012)] published Thu Jan 12, 2012.

Propagation of spiking regularity and double coherence resonance in feedforward networks

Cong Men, Jiang Wang, Ying-Mei Qin, Bin Deng, Kai-Ming Tsang et al.
We investigate the propagation of spiking regularity in noisy feedforward networks (FFNs) based on FitzHugh-Nagumo neuron model systematically. It is found that noise could modulate the transmission of firing rate and spiking regularity. Noise-induced synchronization and synfire-enhanced coherence r ... [Chaos 22, 013104 (2012)] published Tue Jan 10, 2012.

Epidemic threshold and control in a dynamic network

Michael Taylor, Timothy J. Taylor, and Istvan Z. Kiss
In this paper we present a model describing susceptible-infected-susceptible-type epidemics spreading on a dynamic contact network with random link activation and deletion where link activation can be locally constrained. We use and adapt an improved effective degree compartmental modeling framework ... [Phys. Rev. E 85, 016103 ] published .

Reconciling molecular regulatory mechanisms with noise patterns of bacterial metabolic promoters in induced and repressed states

Matthew L. Ferguson, Dominique Le Coq, Matthieu Jules, Stephane Aymerich, Ovidiu Radulescu et al.
Assessing gene expression noise in order to obtain mechanistic insights requires accurate quantification of gene expression on many individual cells over a large dynamic range. We used a unique method based on 2-photon fluorescence fluctuation microscopy to measure directly, at the single cell leve ... [Proc. Natl. Acad. Sci. U.S.A. 109, 155 (2012)] published Fri Jan 6, 2012.

Patterns of synchronization in the hydrodynamic coupling of active colloids

Giovanni M. Cicuta, Enrico Onofri, Marco Cosentino Lagomarsino, and Pietro Cicuta
A system of active colloidal particles driven by harmonic potentials to oscillate about the vertices of a regular polygon, with hydrodynamic coupling between all particles, is described by a piecewise linear model which exhibits various patterns of synchronization. Analytical solutions are obtained ... [Phys. Rev. E 85, 016203 ] published .

Growth, metabolic partitioning, and the size of microorganisms

Christopher P. Kempes, Stephanie Dutkiewicz, and Michael J. Follows
Population growth rate is a fundamental ecological and evolutionary characteristic of living organisms, but individuals must balance the metabolism devoted to biosynthesis and reproduction against the maintenance of existing structure and other functionality. Here we present a mathematical model th ... [Proc. Natl. Acad. Sci. U.S.A. 109, 495 (2012)] published Tue Jan 10, 2012.

Laser-patterned stem-cell bridges in a cardiac muscle model for on-chip electrical conductivity analyses

Zhen Ma, Qiuying Liu, Honghai Liu, Huaxiao Yang, Julie X. Yun et al.
Following myocardial infarction there is an irreversible loss of cardiomyocytes that results in the alteration of electrical propagation in the heart. Restoration of functional electrical properties of the damaged heart muscle is essential to recover from the infarction. While there are a few report ... [Lab Chip 12, 566 (2012)] published Wed Jan 11, 2012.

Photonic polycrystal in the greenish-white scales of the African longhorn beetle Prosopocera lactator (Cerambycidae)

Jean-Francois Colomer, Priscilla Simonis, Annick Bay, Peter Cloetens, Heikki Suhonen et al.
Three-dimensional photonic-crystal grains were found in the scales of the longhorn beetle Prosopocera lactator (Cerambycidae). The local geometric structure can be described as a face-centered-cubic array of spheres, connected by short rods, reminiscent of the ball-and-stick models used by solid-sta ... [Phys. Rev. E 85, 011907 ] published .

Evidence for formation of DNA repair centers and dose-response nonlinearity in human cells

Teresa Neumaier, Joel Swenson, Christopher Pham, Aris Polyzos, Alvin T. Lo et al.
The concept of DNA "repair centers" and the meaning of radiation-induced foci (RIF) in human cells have remained controversial. RIFs are characterized by the local recruitment of DNA damage sensing proteins such as p53 binding protein (53BP1). Here, we provide strong evidence for the existence of r ... [Proc. Natl. Acad. Sci. U.S.A. 109, 443 (2012)] published Tue Jan 10, 2012.

Secreted Wingless-interacting molecule (Swim) promotes long-range signaling by maintaining Wingless solubility

Kimberly A. Mulligan, Christophe Fuerer, Wendy Ching, Matt Fish, Karl Willert et al.
Lipid-modified Wnt/Wingless (Wg) proteins can signal to their target cells in a short- or long-range manner. How these hydrophobic proteins travel through the extracellular environment remains an outstanding question. Here, we report on a Wg binding protein, Secreted Wg-interacting molecule (Swim), ... [Proc. Natl. Acad. Sci. U.S.A. 109, 370 (2012)] published Tue Jan 10, 2012.

Plant extracellular ATP signalling: new insight from proteomics

Stephen Chivasa and Antoni R. Slabas
Complex signalling systems have evolved in multicellular organisms to enable cell-to-cell communication during growth and development. In plants, cell communication via the extracellular matrix (apoplast) controls many processes vital for plant survival. Secretion of ATP into the extracellular matri ... [Mol. BioSyst. 8, 445 (2012)] published Thu Jan 12, 2012.

Noise effects in nonlinear biochemical signaling

Neda Bostani, David A. Kessler, Nadav M. Shnerb, Wouter-Jan Rappel, and Herbert Levine
It has been generally recognized that stochasticity can play an important role in the information processing accomplished by reaction networks in biological cells. Most treatments of that stochasticity employ Gaussian noise even though it is a priori obvious that this approximation can violate physi ... [Phys. Rev. E 85, 011901 ] published .

Properties of underwater acoustic communication channels in shallow water

T. C. Yang
Underwater acoustic channels are band-limited and reverberant, posing many obstacles to reliable, phase-coherent acoustic communications. While many high frequency communication experiments have been conducted in shallow water, few have carried out systematic studies on the channel properties at a t ... [J. Acoust. Soc. Am. 131, 129 (2012)] published Fri Jan 13, 2012.

Cellular ability to sense spatial gradients in the presence of multiple competitive ligands

Shu-Hao Liou and Chia-Chu Chen
Many eukaryotic and prokaryotic cells can exhibit remarkable sensing ability under small gradients of chemical compounds. In this study, we approach this phenomenon by considering the contribution of multiple ligands to the chemical kinetics within the Michaelis-Menten model. This work was inspired ... [Phys. Rev. E 85, 011904 ] published .

Depth measurements of drilled holes in bone by laser triangulation for the field of oral implantology

D. Quest, C. Gayer, and P. Hering
Laser osteotomy is one possible method of preparing beds for dental implants in the human jaw. A major problem in using this contactless treatment modality is the lack of haptic feedback to control the depth while drilling the implant bed. A contactless measurement system called laser triangulation ... [J. Appl. Phys. 111, 013106 (2012)] published Thu Jan 12, 2012.

The transparent crab: preparation and nanostructural implications for bioinspired optically transparent nanocomposites

Md. Iftekhar Shams, Masaya Nogi, Lars A. Berglund, and Hiroyuki Yano
An optically transparent crab-shell with an intact original shape and substantial morphological detail is presented. Inorganic calcium carbonate particles, proteins, lipids and pigments are removed from a native crab-shell, and the remaining chitin nanofibrous structure is impregnated by a monomer a ... [Soft Matter 8, 1369 (2012)] published Thu Jan 12, 2012.

A viscoelastic regime in dilute hydrophobin monolayers

Elodie Aumaitre, Simon Wongsuwarn, Damiano Rossetti, Nicholas D. Hedges, Andrew R. Cox et al.
We show unexpected viscoelastic response in dilute conditions for hydrophobin layers subjected to compression in a Langmuir trough. The surface pressure, surface dilatational and shear viscoelasticity, and layer thickness, are probed by combining four different experimental techniques: Wilhelmy plat ... [Soft Matter 8, 1175 (2012)] published Wed Jan 4, 2012.

Bubblegrams Reveal the Inner Body of Bacteriophage KZ

Weimin Wu, Julie A. Thomas, Naiqian Cheng, Lindsay W. Black, and Alasdair C. Steven
Dense packing of macromolecules in cellular compartments and higher-order assemblies makes it difficult to pick out even quite large components in electron micrographs, despite nominally high resolution. Immunogold labeling and histochemical procedures offer ways to map certain components but are li ... [Science 335, 182 ] published .

Tail-assisted pitch control in lizards, robots and dinosaurs

Thomas Libby, Talia Y. Moore, Evan Chang-Siu, Deborah Li, Daniel J. Cohen et al.
In 1969, a palaeontologist proposed that theropod dinosaurs used their tails as dynamic stabilizers during rapid or irregular movements, contributing to their depiction as active and agile predators. Since then the inertia of swinging appendages has been implicated in stabilizing human walking, aid ... [Nature 481, 181 (2012)] published Thu Jan 12, 2012.

Hierarchical fiber bundle model to investigate the complex architectures of biological materials

Nicola M. Pugno, Federico Bosia, and Tamer Abdalrahman
The mechanics of fiber bundles has been widely studied in the literature, and fiber bundle models in particular have provided a wealth of useful analytical and numerical results for modeling ordinary materials. These models, however, are inadequate to treat bioinspired nanostructured materials, wher ... [Phys. Rev. E 85, 011903 ] published .

Modeling of thermal effects in antivascular ultrasound therapy

Benjamin J. Levenback, Chandra M. Sehgal, and Andrew K. W. Wood
Antivascular ultrasound consisting of low-intensity sonication in the presence of circulating microbubbles of an ultrasound contrast agent has been demonstrated to disrupt blood flow in solid cancers. In this study a mathematical framework is described for the microbubble-induced heating that occurs ... [J. Acoust. Soc. Am. 131, 540 (2012)] published Fri Jan 13, 2012.

Biocompatible noisy nanotopographies with specific directionality for controlled anisotropic cell cultures

Sandro Meucci, Ilaria Tonazzini, Fabio Beltram, and Marco Cecchini
All cells are exposed to extra-cellular physical stimuli determined by the details of the micro-/nano-environment within which they exist. These stimuli are present in organs and tissues where specific directional signals coexist with biotopographical noise (e.g. cellular debris, residues of apoptot ... [Soft Matter 8, 1109 (2012)] published Wed Jan 4, 2012.

Forced wave motion with internal and boundary damping

Tobias Louw, Scott Whitney, Anu Subramanian, and Hendrik Viljoen
A d'Alembert-based solution of forced wave motion with internal and boundary damping is presented with the specific intention of investigating the transient response. The dynamic boundary condition is a convenient method to model the absorption and reflection effects of an interface without consider ... [J. Appl. Phys. 111, 014702 (2012)] published Fri Jan 6, 2012.

A thermodynamical model for stress-fiber organization in contractile cells

Louis Foucard and Franck J. Vernerey
Cell mechanical adaptivity to external stimuli is vital to many of its biological functions. A critical question is therefore to understand the formation and organization of the stress fibers from which emerge the cell's mechanical properties. By accounting for the mechanical aspects and the viscoel ... [Appl. Phys. Lett. 100, 013702 (2012)] published Wed Jan 4, 2012.

Dual-medium quantitative measurement simulation on cells

Yawei Wang, Weifeng Jin, and Naifei Ren
For research on inhomogeneous cells, we present a simulation method called the dual-medium quantitative (DMQ) measurement simulation method, which is realized by combining phase-shifting digital holography with DMQ analysis. The reliability of this method is confirmed by comparing the simulated pha ... [Appl. Opt. 50, 6440 (2012)] published Tue Jan 3, 2012.

The biosonar field around an Atlantic bottlenose dolphin (Tursiops truncatus)

Whitlow W. L. Au, Brian Branstetter, Patrick W. Moore, and James J. Finneran
The use of remote autonomous passive acoustic recorders (PAR) to determine the distribution of dolphins at a given locations has become very popular. Some investigators are using echolocation clicks to gather information on the presence of dolphins and to identify species. However, in all of these c ... [J. Acoust. Soc. Am. 131, 569 (2012)] published Fri Jan 13, 2012.

Deformation of a single red blood cell in bounded Poiseuille flows

Lingling Shi, Tsorng-Whay Pan, and Roland Glowinski
Deformation of a red blood cell (RBC) in bounded two-dimensional Poiseuille flows is studied by using an immersed boundary method (IBM). An elastic spring model is applied to simulate the skeleton structure of a RBC membrane. As a benchmarking test, the dynamical behavior of a single RBC under a sim ... [Phys. Rev. E 85, 016307 ] published .

Estimating the bending modulus of a FtsZ bacterial-division protein filament

Eric N. Cytrynbaum, Yongnan Devin Li, Jun F. Allard, and Hadi Mehrabian
FtsZ, a cytoskeletal protein homologous to tubulin, is the principle constituent of the division ring in bacterial cells. It is known to have force-generating capacity in vitro and has been conjectured to be the source of the constriction force in vivo. Several models have been proposed to explain t ... [Phys. Rev. E 85, 011902 ] published .

Counterion-induced formation of regular actin bundle networks

Florian Huber, Dan Strehle, and Josef Kas
Dominating the cytoskeletal contribution to cell mechanics and migration, actin and actin-crosslinker systems have attained much attention with regard to rheology and network architecture. In contrast to protein crosslinkers or molecular motorswhich self-assemble and self-organize actin into network ... [Soft Matter 8, 931 (2012)] published Wed Jan 4, 2012.

A single conformational transglutaminase 2 epitope contributed by three domains is critical for celiac antibody binding and effects

Zsofia Simon-Vecsei, Robert Kiraly, Peter Bagossi, Boglarka Toth, Ingrid Dahlbom et al.
The multifunctional, protein cross-linking transglutaminase 2 (TG2) is the main autoantigen in celiac disease, an autoimmune disorder with defined etiology. Glutamine-rich gliadin peptides from ingested cereals, after their deamidation by TG2, induce T-lymphocyte activation accompanied by autoantib ... [Proc. Natl. Acad. Sci. U.S.A. 109, 431 (2012)] published Tue Jan 10, 2012.

Structure-based design of conformation- and sequence-specific antibodies against amyloid beta

Joseph M. Perchiacca, Ali Reza A. Ladiwala, Moumita Bhattacharya, and Peter M. Tessier
Conformation-specific antibodies that recognize aggregated proteins associated with several conformational disorders (e.g., Parkinson and prion diseases) are invaluable for diagnostic and therapeutic applications. However, no systematic strategy exists for generating conformation-specific antibodie ... [Proc. Natl. Acad. Sci. U.S.A. 109, 84 (2012)] published Fri Jan 6, 2012.

Protein-covered silica nano-particles adsorbing onto synthetic vesicles

Federica De Persiis, Camillo La Mesa, and Ramon Pons
Silica nano-particles with surface acid groups were reacted with coupling agents and, then, with lysozyme, to get functionalized entities. The procedure functionalizes surface sites and ensures moderate coverage. The amount of bound lysozyme, estimated from UV-vis, is 5 molecules per nano-particle. ... [Soft Matter 8, 1361 (2012)] published Thu Jan 12, 2012.

Charge-controlled metastable liquidliquid phase separation in protein solutions as a universal pathway towards crystallization

Fajun Zhang, Roland Roth, Marcell Wolf, Felix Roosen-Runge, Maximilian W. A. Skoda et al.
We demonstrate that a metastable liquidliquid phase separation (LLPS) in protein aqueous solutions can be induced by multivalent metal ions at room temperature. We determine the salt and protein partitioning in the two coexisting phases. The structure factor obtained by small angle X-ray scattering ... [Soft Matter 8, 1313 (2012)] published Thu Jan 12, 2012.

Self-assembly of human amylin-derived peptides studied by atomic force microscopy and single molecule force spectroscopy

Juan Jose Valle-Delgado, Inta Liepina, Dmitrijs Lapidus, Raimon Sabate, Salvador Ventura et al.
The self-assembly of peptides and proteins into amyloid fibrils of nanometric thickness and up to several micrometres in length, a phenomenon widely observed in biological systems, has recently aroused a growing interest in nanotechnology and nanomedicine. Here we have applied atomic force microscop ... [Soft Matter 8, 1234 (2012)] published Wed Jan 4, 2012.

Interactions between CD44 protein and hyaluronan: insights from the computational study

Wojciech Plazinski and Agnieszka Knys-Dzieciuch
CD44 is a protein, being a major cell surface receptor for hyaluronan (HA). Molecular modeling investigation was carried out on the murine CD44 in complex with a HA heptasaccharide in order to: (i) elucidate the nature and dynamics of interactions between the HA chain and CD44; (ii) find out if the ... [Mol. BioSyst. 8, 543 (2012)] published Thu Jan 12, 2012.

A triple helical structure supported solely by CHO hydrogen bonding

Kwang-Ming Lee, Jack C. C. Chen, Hsing-Yin Chen, and Ivan J. B. Lin
A novel triple helical structure that is self-assembled by cationic molecules, 1-acetamido-3-(2-pyrazinyl)-imidazolium, is reported. The computational analysis underpins that the formation of the triple helix is driven by CHO hydrogen bonding. ... [Chem. Commun. 48, 1242 (2012)] published Mon Jan 9, 2012.

Design, synthesis and protein-targeting properties of thioether-linked hydrogen bond surrogate helices

Andrew B. Mahon and Paramjit S. Arora
Appropriately-placed hydrogen bond surrogates have been demonstrated to efficiently nucleate helical conformations. Herein we describe an efficient method for the synthesis of thioether-based hydrogen bond surrogate (teHBS) helices. A teHBS helix is shown to adopt a stable conformation and target it ... [Chem. Commun. 48, 1416 (2012)] published Thu Jan 12, 2012.

2D amyloid aggregation of human islet amyloid polypeptide at the solidliquid interface

Ye-Ping Yu, Shuai Zhang, Qian Liu, Yan-Mei Li, Chen Wang et al.
Protein misfolding, aggregation, and amyloid deposits are the common hallmarks of amyloid diseases, such as Alzheimer's disease, type 2 diabetes mellitus (T2DM), Huntington disease, prion disease, and Parkinson's disease. In the case of T2DM, the aggregation of human islet amyloid polypeptide (hIAPP ... [Soft Matter 8, 1616 (2012)] published Thu Jan 12, 2012.

Direct characterization of protein oligomers and their quaternary structures by single-molecule FRET

Cheolhee Kim, Jae Yeol Kim, Seung Hyeon Kim, Byung Il Lee, and Nam Ki Lee
Using a single-molecule method, we directly distinguish among oligomers from monomers to tetramers and determine their quaternary structures. Using this method, we found that RecR forms a stable dimer and its oligomeric form is modulated by its own concentration and the interaction with RecO. ... [Chem. Commun. 48, 1138 (2012)] published Fri Jan 6, 2012.

Polymer-monovalent salt-induced DNA compaction studied via single-molecule microfluidic trapping

Weilin Xu and Susan J. Muller
Polymer-monovalent salt-induced single-molecule DNA compaction/condensation in a microfluidic stagnation point flow was studied by analyzing both DNA compaction images and time trajectories. For the whole DNA compaction process we observed three successive steps: Step I, a relaxation process of the ... [Lab Chip 12, 647 (2012)] published Wed Jan 11, 2012.

Identification of the atomic scale structures of the gold-thiol interfaces of molecular nanowires by inelastic tunneling spectroscopy

Firuz Demir and George Kirczenow
We examine theoretically the effects of the bonding geometries at the gold-thiol interfaces on the inelastic tunneling spectra of propanedithiolate (PDT) molecules bridging gold electrodes and show that inelastic tunneling spectroscopy combined with theory can be used to determine these bonding geom ... [J. Chem. Phys. 136, 014703 (2012)] published Thu Jan 5, 2012.

Following aptamerricin specific binding by single molecule recognition and force spectroscopy measurements

Bin Wang, Cunlan Guo, Guojun Chen, Bosoon Park, and Bingqian Xu
Single molecule recognition imaging and dynamic force spectroscopy (DFS) analysis showed strong binding affinity between an aptamer and ricin, which was comparable with antibodyricin interaction. Molecular simulation showed a ricin binding conformation with aptamers and gave different ricin conforma ... [Chem. Commun. 48, 1644 (2012)] published Fri Jan 13, 2012.

DNA duplexes and triplex-forming oligodeoxynucleotides incorporating modified nucleosides forming stable and selective triplexes

Takashi Kanamori, Yoshiaki Masaki, Masahiro Mizuta, Hirosuke Tsunoda, Akihiro Ohkubo et al.
We have previously reported DNA triplexes containing the unnatural base triad G-PPIC3, in which PPI is an indole-fused cytosine derivative incorporated into DNA duplexes and C3 is an abasic site in triplex-forming oligonucleotides (TFOs) introduced by a propylene linker. In this study, we developed ... [Org. Biomol. Chem. 10, 1007 (2012)] published Fri Jan 13, 2012.

Nucleobase recognition at alkaline pH and apparent pK of single DNA bases immobilised within a biological nanopore

Lorenzo Franceschini, Ellina Mikhailova, Hagan Bayley, and Giovanni Maglia
The four DNA bases are recognized in immobilized DNA strands at high alkaline pH by nanopore current recordings. Ionic currents through the biological nanopores are also employed to measure the apparent pK values of single nucleobases within the immobilised DNA strands. ... [Chem. Commun. 48, 1520 (2012)] published Thu Jan 12, 2012.

Regulation of oxidative DNA damage repair by DNA polymerase lambda and MutYH by cross-talk of phosphorylation and ubiquitination

Enni Markkanen, Barbara van Loon, Elena Ferrari, Jason L. Parsons, Grigory L. Dianov et al.
It is of pivotal importance for genome stability that repair DNA polymerases (Pols), such as Pols lambda and beta, which all exhibit considerably reduced fidelity when replicating undamaged DNA, are tightly regulated, because their misregulation could lead to mutagenesis. Recently, we found that th ... [Proc. Natl. Acad. Sci. U.S.A. 109, 437 (2012)] published Tue Jan 10, 2012.

Resolution limit for DNA barcodes in the Odijk regime

Yanwei Wang, Wes F. Reinhart, Douglas R. Tree, and Kevin D. Dorfman
We develop an approximation for the probability of optically resolving two fluorescent labels on the backbone of a DNA molecule confined in a nanochannel in the Odijk regime as a function of the fluorescence wavelength, channel size, and the properties of the DNA (persistence length and effective wi ... [Biomicrofluidics 6, 014101 (2012)] published Tue Jan 3, 2012.

An immersed boundary method for Brownian dynamics simulation of polymers in complex geometries: Application to DNA flowing through a nanoslit with embedded nanopits

Yu Zhang, Juan J. de Pablo, and Michael D. Graham
This work presents an immersed boundary method that allows fast Brownian dynamics simulation of solutions of polymer chains and other Brownian objects in complex geometries with fluctuating hydrodynamics. The approach is based on the general geometry Ewald-like method, which solves the Stokes equati ... [J. Chem. Phys. 136, 014901 (2012)] published Wed Jan 4, 2012.

Low-energy electron scattering with the purine bases of DNA/RNA using the R-matrix method

Amar Dora, Lilianna Bryjko, Tanja van Mourik, and Jonathan Tennyson
R-matrix calculations on electron collisions with the purine bases found in DNA and RNA (i.e., adenine and guanine) are presented. Resonant anion states of these systems are identified by employing different approximation levels of ab initio theoretical methods, such as the static exchange, the stat ... [J. Chem. Phys. 136, 024324 (2012)] published Fri Jan 13, 2012.

On binding of DNA-bending proteins to DNA minicircles

Shlomi Medalion and Yitzhak Rabin
We present a theoretical study of binding of DNA-bending proteins to circular DNA, using computer simulations of the wormlike chain model of DNA. We find that the binding affinity is affected by the bending elasticity and the conformational entropy of the polymer and that while protein adsorption is ... [J. Chem. Phys. 136, 025102 (2012)] published Tue Jan 10, 2012.

Heat shock protein 90's mechanochemical cycle is dominated by thermal fluctuations

Christoph Ratzke, Felix Berkemeier, and Thorsten Hugel
The molecular chaperone and heat shock protein 90 (Hsp90) exists mainly as a homodimer in the cytoplasm. Each monomer has an ATPase in its N-terminal domain and undergoes large conformational changes during Hsp90's mechanochemical cycle. The three-color single-molecule assay and data analysis prese ... [Proc. Natl. Acad. Sci. U.S.A. 109, 161 (2012)] published Fri Jan 6, 2012.

Conformational properties of cardiolipin-bound cytochrome c

Jonas Hanske, Jason R. Toffey, Anna M. Morenz, Amber J. Bonilla, Katherine H. Schiavoni et al.
Interactions of cytochrome c (cyt c) with cardiolipin (CL) are important for both electron transfer and apoptotic functions of this protein. A sluggish peroxidase in its native state, when bound to CL, cyt c catalyzes CL peroxidation, which contributes to the protein apoptotic release. The heteroge ... [Proc. Natl. Acad. Sci. U.S.A. 109, 125 (2012)] published Fri Jan 6, 2012.

Stabilized G protein binding site in the structure of constitutively active metarhodopsin-II

Xavier Deupi, Patricia Edwards, Ankita Singhal, Benjamin Nickle, Daniel Oprian et al.
G protein-coupled receptors (GPCR) are seven transmembrane helix proteins that couple binding of extracellular ligands to conformational changes and activation of intracellular G proteins, GPCR kinases, and arrestins. Constitutively active mutants are ubiquitously found among GPCRs and increase the ... [Proc. Natl. Acad. Sci. U.S.A. 109, 119 (2012)] published Fri Jan 6, 2012.

Structure of a methyl-coenzyme M reductase from Black Sea mats that oxidize methane anaerobically

Seigo Shima, Martin Krueger, Tobias Weinert, Ulrike Demmer, Jrg Kahnt et al.
The anaerobic oxidation of methane (AOM) with sulphate, an area currently generating great interest in microbiology, is accomplished by consortia of methanotrophic archaea (ANME) and sulphate-reducing bacteria. The enzyme activating methane in methanotrophic archaea has tentatively been identified ... [Nature 481, 98 (2012)] published Fri Jan 6, 2012.

Spectroscopic analysis of immobilised redox enzymes under direct electrochemical control

Philip A. Ash and Kylie A. Vincent
This article reviews recent developments in spectroscopic analysis of electrode-immobilised enzymes under direct, unmediated electrochemical control. These methods unite the suite of spectroscopic methods available for characterisation of structural, electronic and coordination changes in proteins w ... [Chem. Commun. 48, 1400 (2012)] published Thu Jan 12, 2012.

Disordered form of the scaffold protein IscU is the substrate for iron-sulfur cluster assembly on cysteine desulfurase

Jin Hae Kim, Marco Tonelli, and John L. Markley
The scaffold protein for iron-sulfur cluster assembly, apo-IscU, populates two interconverting conformational states, one disordered (D) and one structured (S) as revealed by extensive NMR assignments. At pH 8 and 25 degrees C, approximately 70% of the protein is S, and the lifetimes of the states ... [Proc. Natl. Acad. Sci. U.S.A. 109, 454 (2012)] published Tue Jan 10, 2012.

Nonplanar peptide bonds in proteins are common and conserved but not biased toward active sites

Donald S. Berkholz, Camden M. Driggers, Maxim V. Shapovalov, Roland L. Dunbrack, and P. Andrew Karplus
The planarity of peptide bonds is an assumption that underlies decades of theoretical modeling of proteins. Peptide bonds strongly deviating from planarity are considered very rare features of protein structure that occur for functional reasons. Here, empirical analyses of atomic-resolution protein ... [Proc. Natl. Acad. Sci. U.S.A. 109, 449 (2012)] published Tue Jan 10, 2012.

An unanticipated architecture of the 750-kDa holoenzyme of 3-methylcrotonyl-CoA carboxylase

Christine S. Huang, Peng Ge, Z. Hong Zhou, and Liang Tong
3-Methylcrotonyl-CoA carboxylase (MCC), a member of the biotin-dependent carboxylase superfamily, is essential for the metabolism of leucine, and deficient mutations in this enzyme are linked to methylcrotonylglycinuria (MCG) and other serious diseases in humans. MCC has strong sequence conservatio ... [Nature 481, 219 (2012)] published Thu Jan 12, 2012.

Binary complex crystal structure of DNA polymerase beta reveals multiple conformations of the templating 8-oxoguanine lesion

Vinod K. Batra, David D. Shock, William A. Beard, Charles E. McKenna, and Samuel H. Wilson
Oxidation of genomic DNA forms the guanine lesion 7,8-dihydro-8-oxoguanine (8-oxoG). When in the template base position during DNA synthesis the 8-oxoG lesion has dual coding potential by virtue of its anti- and syn-conformations, base pairing with cytosine and adenine, respectively. This impacts m ... [Proc. Natl. Acad. Sci. U.S.A. 109, 113 (2012)] published Fri Jan 6, 2012.

The proteasomal subunit Rpn6 is a molecular clamp holding the core and regulatory subcomplexes together

Ganesh Ramnath Pathare, Istvan Nagy, Stefan Bohn, Pia Unverdorben, Agnes Hubert et al.
Proteasomes execute the degradation of most cellular proteins. Although the 20S core particle (CP) has been studied in great detail, the structure of the 19S regulatory particle (RP), which prepares ubiquitylated substrates for degradation, has remained elusive. Here, we report the crystal structur ... [Proc. Natl. Acad. Sci. U.S.A. 109, 149 (2012)] published Fri Jan 6, 2012.

Effect of glycerol and dimethyl sulfoxide on the phase behavior of lysozyme: Theory and experiments

Christoph Gogelein, Dana Wagner, Frederic Cardinaux, Gerhard Nagele, and Stefan U. Egelhaaf
Salt, glycerol, and dimethyl sulfoxide (DMSO) are used to modify the properties of protein solutions. We experimentally determined the effect of these additives on the phase behavior of lysozyme solutions. Upon the addition of glycerol and DMSO, the fluidsolid transition and the gasliquid coexistenc ... [J. Chem. Phys. 136, 015102 (2012)] published Wed Jan 4, 2012.

Dynamics of highly concentrated protein solutions around the denaturing transition

Marcus Hennig, Felix Roosen-Runge, Fajun Zhang, Stefan Zorn, Maximilian W. A. Skoda et al.
Using both quasi-elastic and fixed-window neutron spectroscopy, we study the dynamics of highly concentrated aqueous protein solutions of bovine serum albumin around the denaturing transition. For the temperature range 280 K < T < 370 K, the total mean-squared displacement is recorded. Below and ab ... [Soft Matter 8, 1628 (2012)] published Thu Jan 12, 2012.

Dynamic structure factor of vibrating fractals: Proteins as a case study

Shlomi Reuveni, Joseph Klafter, and Rony Granek
We study the dynamic structure factor S(k,t) of proteins at large wave numbers k, kR>>1, where R is the gyration radius. At this regime measurements are sensitive to internal dynamics, and we focus on vibrational dynamics of folded proteins. Exploiting the analogy between proteins and fractals, we p ... [Phys. Rev. E 85, 011906 ] published .

Viscosity and diffusion: crowding and salt effects in protein solutions

Marco Heinen, Fabio Zanini, Felix Roosen-Runge, Diana Fedunova, Fajun Zhang et al.
We report on a joint experimentaltheoretical study of collective diffusion in, and static shear viscosity of solutions of bovine serum albumin (BSA) proteins, focusing on the dependence on protein and salt concentration. Data obtained from dynamic light scattering and rheometric measurements are com ... [Soft Matter 8, 1404 (2012)] published Thu Jan 12, 2012.

Exploring one-state downhill protein folding in single molecules

Jianwei Liu, Luis A. Campos, Michele Cerminara, Xiang Wang, Ravishankar Ramanathan et al.
A one-state downhill protein folding process is barrierless at all conditions, resulting in gradual melting of native structure that permits resolving folding mechanisms step-by-step at atomic resolution. Experimental studies of one-state downhill folding have typically focused on the thermal denat ... [Proc. Natl. Acad. Sci. U.S.A. 109, 179 (2012)] published Fri Jan 6, 2012.

Cooperative macromolecular device revealed by meta-analysis of static and time-resolved structures

Zhong Ren, Vukica Srajer, James E. Knapp, and William E. Royer
Here we present a meta-analysis of a large collection of static structures of a protein in the Protein Data Bank in order to extract the progression of structural events during protein function. We apply this strategy to the homodimeric hemoglobin HbI from Scapharca inaequivalvis. We derive a simpl ... [Proc. Natl. Acad. Sci. U.S.A. 109, 107 (2012)] published Fri Jan 6, 2012.

Revealing conformational substates of lipidated N-Ras protein by pressure modulation

Shobhna Kapoor, Gemma Triola, Ingrid R. Vetter, Mirko Erlkamp, Herbert Waldmann et al.
Regulation of protein function is often linked to a conformational switch triggered by chemical or physical signals. To evaluate such conformational changes and to elucidate the underlying molecular mechanisms of subsequent protein function, experimental identification of conformational substates a ... [Proc. Natl. Acad. Sci. U.S.A. 109, 460 (2012)] published Tue Jan 10, 2012.

Nuclear magnetic resonance investigation of dynamics in poly(ethylene oxide)-based lithium polyether-ester-sulfonate ionomers

David J. Roach, Shichen Dou, Ralph H. Colby, and Karl T. Mueller
Nuclear magnetic resonance spectroscopy has been utilized to investigate the dynamics of poly(ethylene oxide)-based lithium sulfonate ionomer samples that have low glass transition temperatures. H and Li spin-lattice relaxation times (T) of the bulk polymer and lithium ions, respectively, were measu ... [J. Chem. Phys. 136, 014510 (2012)] published Fri Jan 6, 2012.

Weak-to-strong confinement transition of semi-flexible macromolecules in slit and in channel

Peter Cifra
We compare confinement of stiff macromolecule in channel and in slit. Whereas in the channel a distinct and established transition exists, we elucidate here an ongoing controversy reported from previous experiment and simulation on existence of such transition in the slit. Our extensive molecular si ... [J. Chem. Phys. 136, 024902 (2012)] published Mon Jan 9, 2012.

Multi-scale modeling of diffusion-controlled reactions in polymers: Renormalisation of reactivity parameters

Ralf Everaers and Angelo Rosa
The quantitative description of polymeric systems requires hierarchical modeling schemes, which bridge the gap between the atomic scale, relevant to chemical or biomolecular reactions, and the macromolecular scale, where the longest relaxation modes occur. Here, we use the formalism for diffusion-co ... [J. Chem. Phys. 136, 014902 (2012)] published Wed Jan 4, 2012.

Phase diagram of two-dimensional systems of dipole-like colloids

Heiko Schmidle, Carol K. Hall, Orlin D. Velev, and Sabine H. L. Klapp
Based on Discontinuous Molecular Dynamics (DMD) simulations we present a phase diagram of two-dimensional nano-particles with dipole-like short-ranged interactions. Similar to systems with true, long-ranged dipolar interactions the present system undergoes a transition from an isotropic fluid phase ... [Soft Matter 8, 1521 (2012)] published Thu Jan 12, 2012.

Comparison of the kinetic friction of planar neutral and polyelectrolyte polymer brushes using molecular dynamics simulations

Yangpeng Ou, Jeffrey B. Sokoloff, and Mark J. Stevens
We have simulated the relative shear motion of both neutral and polyelectrolyte end-grafted polymer brushes using molecular dynamics. The flexible neutral polymer brush is treated as a bead-spring model, and the polyelectrolyte brush is treated the same way except that each bead is charged and there ... [Phys. Rev. E 85, 011801 ] published .

Isothermal crystallization of poly(3-hydroxybutyrate) studied by terahertz two-dimensional correlation spectroscopy

Hiromichi Hoshina, Shinya Ishii, Yusuke Morisawa, Harumi Sato, Isao Noda et al.
The isothermal crystallization of poly(3-hydroxybutylate) (PHB) was studied by monitoring the temporal evolution of terahertz absorption spectra in conjunction with spectral analysis using two-dimensional correlation spectroscopy. Correlation between the absorption peaks and the sequential order of ... [Appl. Phys. Lett. 100, 011907 (2012)] published Thu Jan 5, 2012.

Nature of curvature coupling of amphiphysin with membranes depends on its bound density

Benoit Sorre, Andrew Callan-Jones, John Manzi, Bruno Goud, Jacques Prost et al.
Cells are populated by a vast array of membrane-binding proteins that execute critical functions. Functions, like signaling and intracellular transport, require the abilities to bind to highly curved membranes and to trigger membrane deformation. Among these proteins is amphiphysin 1, implicated in ... [Proc. Natl. Acad. Sci. U.S.A. 109, 173 (2012)] published Fri Jan 6, 2012.

Membrane labeling and immobilization via copper-free click chemistry

Heidi E. Bostic, Matthew D. Smith, Andrei A. Poloukhtine, Vladimir V. Popik, and Michael D. Best
Copper-free click chemistry was employed to derivatize membrane bilayers. This approach uses an azido-lipid conjugate presented on liposomes, which can be labeled in bioorthogonal fashion via cyclooctyne-tagged reagents. An immobilization-based approach using streptavidin-coated microplates was expl ... [Chem. Commun. 48, 1431 (2012)] published Thu Jan 12, 2012.

Polysaccharide based covalently linked multi-membrane hydrogels

Anandhan Dhanasingh and Jurgen Groll
Layer-by-layer techniques bear great potential for biomaterials as they allow sequential construction of hierarchical constructs. This especially accounts for hydrogels which can be tuned for biochemically, morphologically and mechanically different microenvironments and find numerous applications f ... [Soft Matter 8, 1643 (2012)] published Thu Jan 12, 2012.

Surface-grafted zwitterionic polymers as platforms for functional supported phospholipid membranes

M. Gabriella Santonicola, Mine Memesa, Anna Meszynska, Yujie Ma, and G. Julius Vancso
Polymer brushes grafted from surfaces using controlled polymerization techniques, most notably surface-initiated atom-transfer radical polymerization (SI-ATRP), provide robust and reproducible platforms with precise control of surface properties. These platforms are especially useful in biologically ... [Soft Matter 8, 1556 (2012)] published Thu Jan 12, 2012.

Small polar molecules like glycerol and urea can preserve the fluidity of lipid bilayers under dry conditions

A. Nowacka, S. Douezan, L. Wadso, D. Topgaard, and E. Sparr
Glycerol and urea are examples of small, water-soluble molecules with low vapor pressure that can protect lipid membranes upon dehydration. Both are a part of the Natural Moisturizing Factor in human skin, and are also present in other organisms, where they prevent drying due to osmotic stress. This ... [Soft Matter 8, 1482 (2012)] published Thu Jan 12, 2012.

Structural basis for gating charge movement in the voltage sensor of a sodium channel

Vladimir Yarov-Yarovoy, Paul G. DeCaen, Ruth E. Westenbroek, Chien-Yuan Pan, Todd Scheuer et al.
Voltage-dependent gating of ion channels is essential for electrical signaling in excitable cells, but the structural basis for voltage sensor function is unknown. We constructed high-resolution structural models of resting, intermediate, and activated states of the voltage-sensing domain of the ba ... [Proc. Natl. Acad. Sci. U.S.A. 109, E93 (2012)] published Tue Jan 10, 2012.

Biofilm detachment by self-collapsing air microbubbles: a potential chemical-free cleaning technology for membrane biofouling

Ashutosh Agarwal, Huijuan Xu, Wun Jern Ng, and Yu Liu
Microbubbles (MBs) have been known for their ability to generate pressure waves through shrinking and subsequent self-collapsing phenomenon. In the present study, we have investigated the potential of air MBs for biofilm detachment from a nylon membrane surface in comparison to chemical cleaning by ... [J. Mater. Chem. 22, 2203 (2012)] published Wed Jan 11, 2012.

Development of the first sphingomyelin biomimetic stationary phase for immobilized artificial membrane (IAM) chromatography

Dieter Verzele, Frederic Lynen, Mike De Vrieze, Adrian G. Wright, Melissa Hanna-Brown et al.
A prototype sphingomyelin stationary phase for Immobilized Artificial Membrane (IAM) chromatography was synthesized by an ultra-short, solid-phase inspired methodology, in which an oxidative release monitoring strategy played a vital role. Evaluated in a proof-of-concept model for bloodbrain barrier ... [Chem. Commun. 48, 1162 (2012)] published Fri Jan 6, 2012.

Open structure of the Ca gating ring in the high-conductance Ca-activated K channel

Peng Yuan, Manuel D. Leonetti, Yichun Hsiung, and Roderick MacKinnon
High-conductance voltage- and Ca-activated K channels function in many physiological processes that link cell membrane voltage and intracellular Ca concentration, including neuronal electrical activity, skeletal and smooth muscle contraction, and hair cell tuning. Like other voltage-dependent K cha ... [Nature 481, 94 (2012)] published Fri Jan 6, 2012.

Structure and dynamics of nano-sized raft-like domains on the plasma membrane

Fernando E. Herrera and Sergio Pantano
Cell membranes are constitutively composed of thousands of different lipidic species, whose specific organization leads to functional heterogeneities. In particular, sphingolipids, cholesterol and some proteins associate among them to form stable nanoscale domains involved in recognition, signaling, ... [J. Chem. Phys. 136, 015103 (2012)] published Thu Jan 5, 2012.

Interaction of lipid vesicle with silver nanoparticle-serum albumin protein corona

Ran Chen, Poonam Choudhary, Ryan N. Schurr, Priyanka Bhattacharya, Jared M. Brown et al.
The physical interaction between a lipid vesicle and a silver nanoparticle (AgNP)-human serum albumin (HSA) protein corona has been examined. Specifically, the binding of AgNPs and HSA was analyzed by spectrophotometry, and the induced conformational changes of the HSA were inferred from circular di ... [Appl. Phys. Lett. 100, 013703 (2012)] published Thu Jan 5, 2012.

Collapse and coacervation of a lamellar phase by inter-headgroup bridging

Antara Pal, P. Bharath, Sudipta G. Dastidar, and V. A. Raghunathan
We report the collapse of an electrostatically swollen surfactant lamellar phase above a critical concentration of an added nonionic surfactant due to hydrogen bonding between the two types of headgroups. At still higher concentrations of the neutral surfactant a temperature-driven lamellar to coace ... [Soft Matter 8, 927 (2012)] published Wed Jan 4, 2012.

Free energy profiles for penetration of methane and water molecules into spherical sodium dodecyl sulfate micelles obtained using the thermodynamic integration method combined with molecular dynamics calculations

K. Fujimoto, N. Yoshii, and S. Okazaki
The free energy profiles, DeltaG(r), for penetration of methane and water molecules into sodium dodecyl sulfate (SDS) micelles have been calculated as a function of distance r from the SDS micelle to the methane and water molecules, using the thermodynamic integration method combined with molecular ... [J. Chem. Phys. 136, 014511 (2012)] published Fri Jan 6, 2012.

Molecular theory of solvation for supramolecules and soft matter structures: application to ligand binding, ion channels, and oligomeric polyelectrolyte gelators

Andriy Kovalenko, Alexander E. Kobryn, Sergey Gusarov, Olga Lyubimova, Xiangjun Liu et al.
We combine the statisticalmechanical 1D/3D-RISM-KH molecular theory of solvation with DFT electronic structure calculations and MD and coarse-grained DPD simulations, and apply them to study association phenomena in synthetic organic soft matter and biomolecular systems. This combined approach from ... [Soft Matter 8, 1508 (2012)] published Thu Jan 12, 2012.

Molecular dynamics simulation study of the water-mediated interaction between zwitterionic and charged surfaces

Changsun Eun and Max L. Berkowitz
We calculated the potential of mean force (PMF) for the interaction between a model zwitterionic bilayer and a model charged bilayer. To understand the role of water, we separated the PMF into two components: one due to direct interaction and the other due to water-mediated interaction. In our calcu ... [J. Chem. Phys. 136, 024501 (2012)] published Mon Jan 9, 2012.

Photodissociation pathways and lifetimes of protonated peptides and their dimers

G. Aravind, B. Klaerke, J. Rajput, Y. Toker, L. H. Andersen et al.
Photodissociation lifetimes and fragment channels of gas-phase, protonated YA (n = 1,2) peptides and their dimers were measured with 266 nm photons. The protonated monomers were found to have a fast dissociation channel with an exponential lifetime of ~200 ns while the protonated dimers show an addi ... [J. Chem. Phys. 136, 014307 (2012)] published Wed Jan 4, 2012.

Phonon-mediated path-interference in electronic energy transfer

Hoda Hossein-Nejad, Alexandra Olaya-Castro, and Gregory D. Scholes
We present a formalism to quantify the contribution of path-interference in phonon-mediated electronic energy transfer. The transfer rate between two molecules is computed by considering the quantum mechanical amplitudes associated with pathways connecting the initial and final sites. This includes ... [J. Chem. Phys. 136, 024112 (2012)] published Fri Jan 13, 2012.

Hydrogen bonds in the nucleobase-gold complexes: Photoelectron spectroscopy and density functional calculations

Guo-Jin Cao, Hong-Guang Xu, Ren-Zhong Li, and Weijun Zheng
The nucleobase-gold complexes were studied with anion photoelectron spectroscopy and density functional calculations. The vertical detachment energies of uracil-Au, thymine-Au, cytosine-Au, adenine-Au, and guanine-Au were estimated to be 3.37 0.08 eV, 3.40 0.08 eV, 3.23 0.08 eV, 3.28 0.08 eV, an ... [J. Chem. Phys. 136, 014305 (2012)] published Tue Jan 3, 2012.

Large Molecules Reveal a Linear Length Scaling for Double Photoionization

T. Hartman, P. N. Juranic, K. Collins, B. Reilly, N. Appathurai et al.
We have measured the ratio of doubly to singly charged parent ions of benzene, naphthalene, anthracene, and pentacene using monochromatized synchrotron radiation up to 30 eV above the corresponding threshold. Our measurements show a striking similarity between the ratio of doubly charged to all pare ... [Phys. Rev. Lett. 108, 023001 ] published .

Amino acid analogues bind to carbon nanotube via pi-pi interactions: Comparison of molecular mechanical and quantum mechanical calculations

Zaixing Yang, Zhigang Wang, Xingling Tian, Peng Xiu, and Ruhong Zhou
Understanding the interaction between carbon nanotubes (CNTs) and biomolecules is essential to the CNT-based nanotechnology and biotechnology. Some recent experiments have suggested that the pi-pi stacking interactions between protein's aromatic residues and CNTs might play a key role in their bindi ... [J. Chem. Phys. 136, 025103 (2012)] published Tue Jan 10, 2012.

Energetics of short hydrogen bonds in photoactive yellow protein

Keisuke Saito and Hiroshi Ishikita
Recent neutron diffraction studies of photoactive yellow protein (PYP) proposed that the H bond between protonated Glu46 and the chromophore [ionized p-coumaric acid (pCA)] was a low-barrier H bond (LBHB). Using the atomic coordinates of the high-resolution crystal structure, we analyzed the energe ... [Proc. Natl. Acad. Sci. U.S.A. 109, 167 (2012)] published Fri Jan 6, 2012.

The reaction mechanism of hydroxyethylphosphonate dioxygenase: a QM/MM study

Likai Du, Jun Gao, Yongjun Liu, Dongju Zhang, and Chengbu Liu
By employing ab initio quantum mechanical/molecular mechanical (QM/MM) and molecular dynamics (MD) simulations, we have provided further evidence against the previously proposed hydroperoxylation or hydroxylation mechanism of hydroxyethylphosphonate dioxygenase (HEPD). HEPD employs an interesting ca ... [Org. Biomol. Chem. 10, 1014 (2012)] published Fri Jan 13, 2012.

Vibrational dynamics of pyrrole via frequency-domain spectroscopy

Alexander Portnov, Michael Epshtein, Salman Rosenwaks, and Ilana Bar
The NH stretch overtones of pyrrole, a key constituent of biologic building blocks, were studied by room temperature photoacoustic and jet-cooled action spectroscopies to unravel their intramolecular dynamics. Contrary to isolated states excited with two and three NH stretch quanta, the one with fou ... [J. Chem. Phys. 136, 024313 (2012)] published Tue Jan 10, 2012.

Experimental and theoretical investigation of the triple differential cross section for electron impact ionization of pyrimidine molecules

J. D. Builth-Williams, S. M. Bellm, D. B. Jones, Hari Chaluvadi, D. H. Madison et al.
Cross-section data for electron impact induced ionization of bio-molecules are important for modelling the deposition of energy within a biological medium and for gaining knowledge of electron driven processes at the molecular level. Triply differential cross sections have been measured for the elec ... [J. Chem. Phys. 136, 024304 (2012)] published Mon Jan 9, 2012.